Contacts of the helix formed by residues 95 - 114 (chain C) in PDB entry 4F2N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 95 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR* 3.9 30.1 - - - +
92C ILE* 2.9 24.4 + - - +
94C GLU* 1.3 80.0 + - - +
96C LYS* 1.3 64.8 + - - +
97C VAL 3.2 3.2 + - - -
98C MET* 3.3 14.6 + - - +
99C PHE* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR 5.6 0.2 - - - -
91C GLY 6.2 1.6 - - - +
92C ILE 3.4 6.1 + - - +
93C ASN* 3.2 20.2 + - - +
94C GLU 3.5 1.2 - - - -
95C SER* 1.3 78.4 - - - +
97C VAL* 1.3 59.4 + - + +
99C PHE* 3.4 22.4 + - + +
100C ASN* 2.7 68.2 + - - +
175C ASN* 6.3 0.8 - - - +
152D PHE* 5.4 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS* 4.1 17.7 - - - -
73C LEU* 3.8 20.9 - - + -
94C GLU 5.4 0.2 + - - -
95C SER 3.2 1.0 - - - -
96C LYS* 1.3 77.3 - - + +
98C MET* 1.3 62.5 + - - +
100C ASN* 3.2 8.3 + - - +
101C GLN* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 4.1 8.1 - - + -
73C LEU* 3.5 49.7 - - + +
74C GLY* 4.1 9.0 - - - -
77C TYR* 4.5 17.0 - - + +
85C ILE* 4.0 24.0 - - + -
89C THR* 3.7 19.5 - - + -
95C SER* 3.3 17.0 + - - +
97C VAL* 1.3 75.5 - - - +
99C PHE* 1.3 67.2 + - - +
101C GLN* 3.2 4.1 + - - +
102C ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ILE* 3.7 23.3 - - + -
89C THR* 3.3 30.6 + - - +
90C THR* 3.7 35.9 - - - -
91C GLY 5.7 0.2 - - - -
95C SER 2.9 16.0 + - - +
96C LYS* 3.6 22.4 - - + +
98C MET* 1.3 76.4 - - - +
100C ASN* 1.3 74.9 + - - +
102C ALA* 3.7 2.4 - - - +
103C ALA* 2.8 51.8 + - + +
176C ALA* 4.4 12.6 - - + -
177C GLY* 4.8 8.5 - - - -
178C CYS 4.9 1.8 - - - -
181C THR* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LYS* 2.7 52.6 + - - +
97C VAL* 3.2 10.2 + - - +
99C PHE* 1.3 82.1 - - - +
101C GLN* 1.3 61.7 + - - +
104C GLN* 3.0 36.3 + - - +
176C ALA* 3.6 14.4 + - - +
152D PHE* 3.4 49.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA 4.1 0.7 - - - +
66C TYR* 3.3 46.9 - - - +
69C LYS* 3.3 41.9 - - + +
70C LEU* 3.9 14.1 - - + +
73C LEU* 4.3 7.4 - - + -
97C VAL* 3.1 24.8 + - + +
98C MET 3.2 4.0 + - - +
100C ASN* 1.3 85.4 - - - +
102C ALA* 1.3 59.2 + - - +
104C GLN* 3.8 1.6 - - - +
105C HIS* 2.9 28.9 + - - +
152D PHE* 4.7 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 3.9 20.8 - - + +
82C ILE* 3.3 15.6 - - + +
85C ILE* 3.8 26.2 - - + -
86C ILE* 3.8 14.1 - - + +
98C MET 2.9 16.7 + - - +
99C PHE* 3.9 3.1 - - - +
101C GLN* 1.3 75.5 - - - +
103C ALA* 1.3 60.2 + - - +
105C HIS* 3.3 0.5 + - - +
106C PHE* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ILE* 3.6 18.9 - - + +
99C PHE* 2.8 37.3 + - + +
102C ALA* 1.3 73.4 - - - +
104C GLN* 1.3 57.9 + - - +
106C PHE* 3.3 1.9 + - - +
107C ASN* 2.8 36.1 + - - +
176C ALA* 3.2 29.4 - - + +
178C CYS* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 3.0 52.2 + - + -
100C ASN 3.0 25.4 + - - +
101C GLN 4.0 0.2 - - - +
103C ALA* 1.3 73.8 - - - +
105C HIS* 1.3 64.8 + - - +
107C ASN* 3.3 8.4 + - - +
108C HIS* 2.8 46.0 + - - -
156C TRP* 3.1 24.4 + - - -
176C ALA* 3.5 17.8 - - + -
193C TRP* 3.3 26.2 - - - +
195C HIS* 5.1 0.2 - - - -
152D PHE* 3.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.9 15.5 - - + +
30C ARG 4.9 1.0 + - - -
33C ALA* 3.8 17.6 - - + +
34C GLU 3.3 27.9 + - - -
36C PRO* 4.5 0.2 - - + -
63C HIS* 2.9 32.1 + + - +
66C TYR* 4.5 6.9 - - + +
67C VAL* 3.6 13.4 - - + +
70C LEU* 4.2 4.5 - - + -
82C ILE* 3.6 33.6 - - + +
101C GLN 2.9 18.3 + - - +
102C ALA* 3.7 5.4 - - - +
103C ALA 3.3 0.2 - - - -
104C GLN* 1.3 76.4 - - - +
106C PHE* 1.3 60.9 + - - +
109C SER* 2.8 47.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 3.7 26.2 - - + -
26C LEU* 3.8 22.9 - - + -
29C LEU* 3.9 14.4 - - + -
82C ILE* 4.2 4.9 - - + +
83C GLU* 3.5 39.0 - - + -
86C ILE* 3.6 12.8 - - + -
102C ALA 2.9 14.0 + - - +
103C ALA 3.6 5.6 - - - +
105C HIS* 1.3 78.2 - - - +
107C ASN* 1.3 78.1 + - - +
109C SER* 3.3 1.4 + - - -
110C PHE* 2.9 34.6 + - + +
158C TRP* 4.4 8.5 - + - -
178C CYS* 3.6 19.1 - - - -
179C PRO* 5.7 0.2 - - + -
180C LEU* 4.9 2.9 - - + -
186C PRO* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA 2.8 26.2 + - - +
104C GLN* 3.3 15.9 + - - +
105C HIS 3.4 0.2 - - - -
106C PHE* 1.3 83.9 - - - +
108C HIS* 1.3 58.3 + - - +
110C PHE* 3.5 2.9 + - - +
111C PHE* 3.0 27.4 + - - +
156C TRP* 3.4 36.3 - - + +
158C TRP* 3.2 29.9 - - + -
176C ALA 3.2 25.5 + - - -
177C GLY 3.7 4.9 + - - -
178C CYS* 3.5 7.1 - - - -
189C THR* 4.3 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS* 3.1 39.6 + + - -
62C HIS* 5.0 1.4 - - - +
63C HIS* 3.5 29.2 - + + +
66C TYR* 3.5 29.8 - + - -
104C GLN* 2.8 36.8 + - - +
107C ASN* 1.3 74.3 - - - +
109C SER* 1.3 65.3 + - - +
111C PHE* 3.2 7.9 + + - +
112C TRP* 3.0 39.0 + + - +
156C TRP* 3.5 21.3 - + - -
191C ASP* 3.4 9.4 + - - -
195C HIS* 3.8 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.1 5.8 - - - -
29C LEU* 3.6 27.1 - - - +
36C PRO* 3.7 11.7 - - - +
63C HIS* 3.3 7.0 - - - -
105C HIS* 2.8 44.3 + - - -
106C PHE 3.8 0.4 - - - -
108C HIS* 1.3 77.3 - - - +
110C PHE* 1.3 63.2 + - - +
112C TRP* 3.5 11.6 + - - +
113C LYS* 3.4 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 3.5 31.4 - - + -
26C LEU* 3.8 14.7 - - + +
106C PHE* 2.9 26.9 + + + +
107C ASN* 3.7 4.0 - - - +
109C SER* 1.3 77.0 - - - +
111C PHE* 1.3 62.6 + - - +
113C LYS* 3.0 16.6 + - - +
114C CYS* 3.1 21.9 + - - -
158C TRP* 3.9 9.2 - + - -
186C PRO* 3.5 20.0 - - + -
187C ILE* 3.5 24.9 - - - -
188C PHE* 3.6 21.5 - - - -
189C THR* 3.8 16.2 - - + -
220C PHE* 3.6 28.5 - + - -
224C MET* 4.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET* 4.0 12.1 - - + -
58C HIS* 4.0 15.7 - + - -
107C ASN 3.0 16.0 + - - +
108C HIS* 3.4 9.6 - + - +
110C PHE* 1.3 74.8 - - - +
112C TRP* 1.3 85.9 + + - +
114C CYS* 3.1 18.7 + - + +
115C LEU* 3.3 40.8 - - + +
156C TRP* 4.0 10.1 - + + -
189C THR* 3.4 34.8 - - + -
190C ALA* 3.9 2.9 - - - -
191C ASP* 3.6 28.7 - - + -
196C ALA* 5.1 0.2 - - + -
208C TYR* 3.5 21.1 - - - -
212C LEU* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PRO* 4.0 16.4 - - + -
38C LEU* 3.7 27.8 - - + -
39C GLY 5.8 0.2 + - - -
40C PHE* 4.1 8.5 - + + -
46C ILE* 4.6 4.0 - - + -
50C MET* 4.7 4.9 - - - -
55C LEU* 3.6 27.6 - - + -
58C HIS* 3.5 42.6 - + + -
59C TYR* 3.7 24.7 - + + -
63C HIS* 3.0 30.5 + + - -
108C HIS* 3.0 28.9 + + + +
109C SER* 3.9 4.0 - - - +
110C PHE 3.3 0.2 - - - -
111C PHE* 1.3 95.5 - + - +
113C LYS* 1.3 62.1 + - + +
115C LEU* 3.3 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.0 18.6 - - + -
36C PRO* 6.5 0.4 - - + -
37C THR 5.7 3.2 + - - -
109C SER 3.4 13.6 + - - +
110C PHE 3.0 9.2 + - - +
112C TRP* 1.3 77.8 - - + +
114C CYS* 1.3 60.4 + - - +
115C LEU 3.2 3.0 + - - +
217C ASP* 3.9 7.6 - - - +
220C PHE* 3.4 59.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PHE* 3.1 42.8 + - - -
111C PHE* 3.1 14.4 + - - +
113C LYS* 1.3 76.1 - - - +
115C LEU* 1.3 60.6 + - + +
187C ILE 4.2 0.7 - - - -
188C PHE* 3.7 35.2 - - + -
189C THR 3.9 5.8 - - - +
216C VAL* 3.4 10.9 - - - +
217C ASP* 2.8 24.5 + - - -
220C PHE* 4.1 15.5 - - - -
221C VAL* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il