Contacts of the helix formed by residues 95 - 114 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D THR* 3.9 26.6 - - - +
92D ILE* 2.9 28.8 + - - +
94D GLU* 1.3 84.4 + - - +
96D LYS* 1.3 62.1 + - - +
97D VAL 3.4 2.7 - - - -
98D MET* 3.3 17.3 + - - +
99D PHE* 2.9 22.5 + - - +
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Residues in contact with LYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D THR 5.7 0.9 - - - +
91D GLY 6.4 0.2 - - - +
92D ILE 3.6 3.7 + - - +
93D ASN* 3.3 18.3 + - - +
94D GLU 3.5 1.6 - - - -
95D SER* 1.3 78.1 - - - +
97D VAL* 1.3 60.4 + - + +
99D PHE* 3.3 35.2 + - + +
100D ASN* 2.9 51.1 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LYS* 4.0 19.3 - - - -
73D LEU* 3.9 19.3 - - + -
95D SER 3.4 0.8 - - - -
96D LYS* 1.3 77.8 - - + +
98D MET* 1.3 63.2 + - - +
100D ASN* 3.3 7.9 + - - +
101D GLN* 3.1 38.7 + - - +
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Residues in contact with MET 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LEU* 4.1 8.5 - - + -
73D LEU* 3.4 49.7 - - + +
74D GLY* 4.1 9.4 - - - -
77D TYR* 4.2 19.3 - - + +
85D ILE* 4.0 17.9 - - + -
89D THR* 3.8 19.7 - - + -
95D SER* 3.3 19.0 + - - +
97D VAL* 1.3 75.8 - - - +
99D PHE* 1.3 66.5 + - - +
101D GLN* 3.2 3.1 + - - +
102D ALA* 2.8 22.7 + - - +
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ILE* 3.7 31.4 - - + -
89D THR* 3.4 31.1 + - - +
90D THR* 3.8 26.0 - - - -
95D SER 2.9 12.4 + - - +
96D LYS* 3.4 32.8 - - + +
98D MET* 1.3 76.6 - - - +
100D ASN* 1.3 72.7 - - - +
102D ALA* 3.7 2.8 - - - +
103D ALA* 2.8 48.3 + - + +
176D ALA* 4.3 13.5 - - + -
177D GLY* 4.6 8.7 - - - -
178D CYS 5.0 1.8 - - - -
181D THR* 4.1 9.4 - - + -
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Residues in contact with ASN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PHE* 3.4 50.6 - - + +
96D LYS* 2.9 44.6 + - - +
97D VAL* 3.7 8.5 - - - +
98D MET 3.3 0.2 - - - -
99D PHE* 1.3 90.2 - - - +
101D GLN* 1.3 62.4 + - - +
104D GLN* 2.9 36.7 + - - +
176D ALA* 3.6 13.2 + - - +
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Residues in contact with GLN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C PHE* 4.5 8.9 - - - -
65D ALA 4.1 0.7 - - - +
66D TYR* 3.3 45.2 - - - +
69D LYS* 3.3 41.2 - - + +
70D LEU* 4.0 15.5 - - + +
73D LEU* 4.2 4.5 - - + -
97D VAL* 3.1 26.6 + - - +
98D MET 3.7 4.3 - - - +
100D ASN* 1.3 86.4 - - - +
102D ALA* 1.3 61.8 + - - +
105D HIS* 3.0 24.9 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 4.0 16.5 - - + +
82D ILE* 3.3 15.8 - - + +
85D ILE* 3.6 30.7 - - + -
86D ILE* 3.8 15.5 - - + +
98D MET 2.8 21.3 + - - +
99D PHE* 3.8 2.9 - - - +
101D GLN* 1.3 72.5 - - - +
103D ALA* 1.3 57.3 + - - +
105D HIS* 3.2 1.0 + - - +
106D PHE* 2.9 25.8 + - - +
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ILE* 3.7 16.3 - - + +
99D PHE* 2.8 38.5 + - + +
102D ALA* 1.3 73.2 - - - +
104D GLN* 1.3 56.6 + - - +
106D PHE* 3.3 1.2 + - - +
107D ASN* 2.7 36.8 + - - +
176D ALA* 3.2 29.4 - - + +
178D CYS* 4.5 5.2 - - + -
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C PHE* 3.9 4.0 - - + -
66D TYR* 3.0 51.8 + - + +
100D ASN 2.9 22.4 + - - +
103D ALA* 1.3 74.0 - - - +
105D HIS* 1.3 66.0 + - - +
107D ASN* 3.2 8.2 + - - +
108D HIS* 2.7 49.2 + - - -
156D TRP* 3.0 24.9 + - - +
176D ALA* 3.5 14.1 - - + -
193D TRP* 3.3 29.1 - - - +
195D HIS* 5.0 0.2 - - - -
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Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.7 15.8 - - + +
30D ARG 4.9 0.8 + - - -
33D ALA* 3.8 17.7 - - + +
34D GLU 3.3 28.3 + - - -
36D PRO* 4.3 1.1 - - + -
63D HIS* 2.9 31.8 + - + +
66D TYR* 4.4 6.8 - - + +
67D VAL* 3.5 16.0 - - + +
70D LEU* 4.3 3.8 - - + -
82D ILE* 3.6 33.6 - - + +
101D GLN 3.0 18.5 + - - +
102D ALA* 3.5 5.8 - - - +
104D GLN* 1.3 75.0 - - - +
106D PHE* 1.3 62.8 + - - +
109D SER* 2.9 44.6 + - - -
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Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 3.7 22.2 - - + -
26D LEU* 3.8 23.6 - - + -
29D LEU* 3.8 13.9 - - + +
82D ILE* 4.2 5.6 - - + +
83D GLU* 3.6 37.5 - - + -
86D ILE* 3.6 15.0 - - + -
102D ALA 2.9 15.8 + - - +
103D ALA 3.6 2.2 - - - +
105D HIS* 1.3 77.7 - - - +
107D ASN* 1.3 76.6 + - - +
109D SER* 3.3 1.9 + - - -
110D PHE* 2.9 32.0 + + + +
158D TRP* 4.3 13.0 - + - -
178D CYS* 3.6 23.6 - - - -
180D LEU* 3.7 11.7 - - + -
186D PRO* 4.7 1.6 - - + -
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Residues in contact with ASN 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ALA 2.7 25.5 + - - +
104D GLN* 3.2 16.4 + - - +
106D PHE* 1.3 83.3 - - - +
108D HIS* 1.3 58.7 + - - +
110D PHE* 3.7 2.5 - - - +
111D PHE* 3.0 27.4 + - - +
156D TRP* 3.4 35.4 - - + +
158D TRP* 3.1 28.6 - - - -
176D ALA 3.2 24.9 + - - -
177D GLY 3.7 5.5 + - - -
178D CYS* 3.5 6.8 - - - -
189D THR* 4.2 1.7 - - - +
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Residues in contact with HIS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D HIS* 3.1 41.1 + + - -
62D HIS* 5.1 0.6 - - - +
63D HIS* 3.5 30.1 - + + +
66D TYR* 3.5 19.0 - + - -
104D GLN* 2.7 55.8 + - - +
107D ASN* 1.3 75.3 - - - +
109D SER* 1.3 60.3 + - - +
111D PHE* 3.1 6.2 + + - +
112D TRP* 2.9 43.9 + + - +
156D TRP* 3.5 12.9 - + - -
191D ASP* 3.4 9.5 + - - -
195D HIS* 3.7 6.9 + - - -
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Residues in contact with SER 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.1 6.5 - - - -
28D HIS* 6.2 0.2 - - - -
29D LEU* 3.5 24.7 - - - +
36D PRO* 3.6 11.0 - - - +
63D HIS* 3.4 12.8 - - - -
105D HIS* 2.9 35.4 + - - -
106D PHE 3.7 3.4 - - - -
108D HIS* 1.3 75.8 - - - +
110D PHE* 1.3 61.4 + - - +
112D TRP* 3.5 12.5 + - - +
113D LYS* 3.3 26.3 + - - +
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Residues in contact with PHE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 3.6 30.3 - - + -
26D LEU* 3.9 17.9 - - + +
106D PHE* 2.9 27.1 + + + +
107D ASN* 3.7 4.3 - - - +
109D SER* 1.3 77.8 - - - +
111D PHE* 1.3 61.1 - - - +
113D LYS* 3.2 15.1 + - - +
114D CYS* 3.3 22.3 + - - -
158D TRP* 4.1 5.4 - + - -
186D PRO* 3.6 19.7 - - + -
187D ILE* 3.5 24.9 - - - -
188D PHE* 3.6 21.3 - - - -
189D THR* 3.6 18.2 - - + -
220D PHE* 3.7 22.7 - + - -
224D MET* 4.3 3.1 - - + -
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Residues in contact with PHE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D MET* 3.9 15.7 - - + -
58D HIS* 4.1 12.3 - + - -
107D ASN 3.0 15.9 + - - +
108D HIS* 3.3 10.3 - + - +
110D PHE* 1.3 76.1 - - - +
112D TRP* 1.3 83.8 + + - +
114D CYS* 3.0 14.6 + - + +
115D LEU* 3.3 46.4 - - + +
156D TRP* 3.9 9.2 - + + -
189D THR* 3.3 34.5 - - + -
190D ALA* 3.7 3.6 - - - -
191D ASP* 3.6 28.5 - - + -
196D ALA* 5.2 0.2 - - + -
208D TYR* 3.5 21.5 - - - -
212D LEU* 4.6 6.1 - - + -
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Residues in contact with TRP 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D PRO* 4.0 7.6 - - + -
38D LEU* 3.6 32.3 - - + -
40D PHE* 4.2 8.6 - + + -
46D ILE* 4.6 5.2 - - + -
50D MET* 4.7 3.1 - - - -
55D LEU* 3.6 29.2 - - + -
58D HIS* 3.6 38.4 - + + -
59D TYR* 3.7 29.1 - + + -
63D HIS* 3.0 30.4 + + - -
108D HIS* 2.9 32.9 + + + +
109D SER* 3.9 7.6 - - - +
110D PHE 3.3 0.2 - - - -
111D PHE* 1.3 94.8 - + - +
113D LYS* 1.3 64.0 + - + +
115D LEU* 3.2 33.3 + - + +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.6 8.1 - - + -
28D HIS* 3.8 29.2 + - + +
36D PRO* 5.8 6.5 - - - -
37D THR 5.3 9.8 + - - -
109D SER 3.3 14.8 + - - +
110D PHE 3.2 9.5 + - - +
112D TRP* 1.3 77.5 - - + +
114D CYS* 1.3 58.7 + - - +
115D LEU 3.2 3.3 + - - +
217D ASP* 4.0 7.3 - - - +
220D PHE* 3.3 56.0 - - + +
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Residues in contact with CYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 3.3 41.9 + - - -
111D PHE* 3.0 13.2 + - - +
113D LYS* 1.3 76.0 - - - +
115D LEU* 1.3 62.2 + - + +
187D ILE 4.3 0.4 - - - -
188D PHE* 3.7 35.0 - - + -
189D THR 3.8 7.2 - - - +
216D VAL* 3.4 11.1 - - - +
217D ASP* 2.8 25.9 + - - +
220D PHE* 4.0 15.5 - - - -
221D VAL* 4.9 0.4 - - - -
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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
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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) + - + + + + + -
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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