Contacts of the helix formed by residues 97 - 114 (chain C) in PDB entry 2YF3
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 ASP 97 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 5.0 2.1 - - - +
27C GLU 5.7 0.4 + - - -
95C GLY 4.0 2.6 + - - -
96C ILE* 1.3 70.2 - - - +
98C ALA* 1.3 63.2 + - - +
99C ASP* 2.9 26.4 + - - +
100C ALA* 3.2 24.9 + - + +
101C VAL* 3.3 15.8 + - - +
141C LEU* 3.8 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 3.8 9.5 - - + +
88C TYR* 3.6 34.1 - - + +
91C LEU* 3.7 32.0 - - + +
92C ASP 5.8 0.2 - - - +
96C ILE 3.0 6.3 + - - +
97C ASP* 1.3 69.5 + - - +
99C ASP* 1.3 61.2 + - - +
101C VAL* 3.8 4.3 - - - +
102C PHE* 2.9 32.4 + - - +
10D ASN* 4.9 0.2 - - - -
81D ALA* 5.5 0.3 - - - +
84D LEU* 4.5 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 2.7 40.9 + - - +
11C ALA* 3.7 17.0 + - - +
12C GLU* 4.9 3.8 - - - +
88C TYR* 4.3 1.0 + - - -
97C ASP* 2.9 11.1 + - - +
98C ALA* 1.3 76.1 - - - +
100C ALA* 1.3 59.3 + - - +
102C PHE* 3.9 0.6 - - - +
103C ALA* 2.9 31.8 + - - +
10D ASN* 3.1 31.7 + - - +
13D ARG* 5.0 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASP* 3.2 27.7 + - + +
99C ASP* 1.3 80.6 - - - +
101C VAL* 1.3 63.2 + - - +
103C ALA* 3.5 7.3 + - - +
104C GLU* 3.4 19.1 + - - +
137C VAL* 3.9 21.0 - - + +
141C LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.9 2.9 - - + -
96C ILE* 3.5 32.3 - - + -
97C ASP 3.3 5.9 + - - +
98C ALA* 3.9 7.6 - - - +
100C ALA* 1.3 77.5 - - - +
102C PHE* 1.3 62.7 + - - +
104C GLU* 3.1 6.8 + - - +
105C VAL* 3.0 20.4 + - - +
134C VAL* 4.0 28.9 - - + -
137C VAL* 4.0 19.7 - - + -
138C ILE* 4.6 1.1 - - + -
77D ALA* 3.6 27.6 - - + +
81D ALA* 3.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ALA 2.9 18.2 + - - +
99C ASP 3.9 2.0 - - - +
101C VAL* 1.3 75.7 - - - +
103C ALA* 1.3 52.9 + - - +
105C VAL* 3.2 3.9 + - + +
106C HIS* 2.7 33.5 + - + +
10D ASN* 3.1 48.0 - - + +
13D ARG* 3.8 23.3 - - + -
14D LEU* 3.5 17.5 - - + -
81D ALA* 4.1 15.0 - - + +
84D LEU* 3.8 23.3 - - + -
85D TYR* 3.5 48.7 - + - -
88D TYR* 4.0 8.1 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
99C ASP 2.9 19.5 + - - +
100C ALA* 3.7 7.9 - - - +
102C PHE* 1.3 77.9 - - - +
104C GLU* 1.3 58.0 + - - +
106C HIS* 3.8 7.3 - - - +
107C ARG* 3.0 26.7 + - - +
10D ASN* 5.2 0.2 + - - -
13D ARG* 4.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ALA 3.4 2.8 + - - +
101C VAL 3.1 8.5 + - - +
103C ALA* 1.3 77.3 - - - +
105C VAL* 1.3 64.4 + - - +
107C ARG* 2.9 39.2 + - - +
108C ALA* 3.2 20.4 + - - +
132C ALA* 4.0 4.4 - - + +
133C ASP* 2.6 44.5 + - - +
134C VAL* 4.5 3.1 - - + +
137C VAL* 3.7 29.4 - - + -
140C ARG* 4.9 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL 3.0 15.3 + - - +
102C PHE* 3.7 8.5 - - - +
104C GLU* 1.3 74.3 - - - +
106C HIS* 1.3 65.6 + - - +
108C ALA* 3.2 3.2 + - - +
109C ASN* 2.9 42.7 + - - +
132C ALA* 4.1 18.8 - - + -
134C VAL* 4.3 8.3 - - + -
78D HIS* 4.3 10.8 - - + +
81D ALA* 3.9 20.9 - - + +
82D ASP* 3.5 24.7 - - - +
85D TYR* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 2.7 22.0 + - + +
103C ALA 3.8 5.2 - - - +
105C VAL* 1.3 72.7 - - - +
107C ARG* 1.3 56.3 + - - +
110C LEU* 2.7 51.8 + - + +
13D ARG* 3.1 59.2 - - + +
16D GLU* 2.8 25.5 + - - -
17D PHE* 4.1 8.5 - - + -
85D TYR* 2.7 40.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA 3.0 18.1 + - - +
104C GLU* 2.9 41.7 + - - +
105C VAL 3.3 0.4 - - - -
106C HIS* 1.3 77.3 - - - +
108C ALA* 1.3 67.4 - - - +
110C LEU* 4.1 4.3 - - - +
111C SER* 3.0 39.4 + - - -
130C ARG* 3.1 30.5 + - - +
131C PRO 3.1 22.8 + - - -
132C ALA* 3.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU 3.2 8.9 + - - +
105C VAL 3.7 6.3 - - - +
107C ARG* 1.3 92.0 - - - +
109C ASN* 1.3 63.0 + - - +
111C SER* 3.8 0.4 - - - -
112C LYS* 3.0 12.6 + - - +
129C TRP* 2.9 35.9 + - + +
130C ARG 4.0 5.2 - - - +
132C ALA* 3.5 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C VAL* 2.9 39.1 + - - +
106C HIS 3.9 2.0 - - - +
108C ALA* 1.3 78.2 - - - +
110C LEU* 1.3 64.5 + - - +
112C LYS* 3.3 9.5 + - - +
113C ALA* 3.0 22.3 + - - +
129C TRP* 5.9 1.2 - - - -
17D PHE* 3.7 23.5 - - + -
82D ASP* 5.2 1.2 + - - -
85D TYR* 3.5 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C HIS* 2.7 34.0 + - + +
107C ARG* 4.1 4.3 - - - +
109C ASN* 1.3 72.6 - - - +
111C SER* 1.3 63.4 + - - +
113C ALA* 3.2 14.6 + - + +
114C SER* 3.2 13.5 + - - -
16D GLU* 3.6 35.9 - - + +
17D PHE* 4.3 18.1 - - - -
20D ALA* 3.9 27.5 - - + +
85D TYR* 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.0 29.1 + - - -
108C ALA* 3.8 4.9 - - - -
110C LEU* 1.3 77.0 - - - +
112C LYS* 1.3 60.6 + - - +
114C SER* 2.7 26.2 + - - -
126C PRO* 3.2 15.9 - - - +
129C TRP* 3.3 19.3 - - - +
130C ARG 5.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA 3.0 12.8 + - - +
109C ASN* 3.3 9.6 + - - +
111C SER* 1.3 74.6 - - - +
113C ALA* 1.3 59.1 + - - +
115C GLY 3.0 18.5 + - - -
122C LYS* 6.1 2.8 - - - +
123C GLN* 3.1 46.0 + - + -
124C LEU 3.2 8.7 - - - +
125C LYS* 4.1 30.6 - - + +
126C PRO* 3.9 3.8 - - - -
129C TRP* 3.5 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASN 3.0 13.3 + - - +
110C LEU* 3.2 13.9 + - - +
112C LYS* 1.3 76.9 - - - +
114C SER* 1.3 58.4 + - - +
115C GLY 3.2 4.0 + - - +
123C GLN* 3.6 22.2 + - - +
17D PHE* 4.2 6.7 - - + -
20D ALA* 4.2 26.4 - - + +
21D ILE* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU 3.2 8.9 + - - -
111C SER* 2.7 23.1 + - - -
112C LYS 3.1 0.2 + - - -
113C ALA* 1.3 73.1 - - - +
115C GLY* 1.3 65.2 + - - +
126C PRO* 3.9 11.0 - - - +
20D ALA* 6.2 0.7 - - - -
----------------------------------------------------------
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