Contacts of the helix formed by residues 92 - 107 (chain C) in PDB entry 3P71
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 TYR 92 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C CYS* 3.8 18.8 - - - -
60C GLY 2.9 12.9 + - - +
61C GLN* 5.2 0.2 - - - -
62C PHE* 3.6 16.2 - - + -
63C HIS* 3.4 33.2 - + - -
91C TYR* 1.3 97.8 - + + +
93C SER* 1.3 57.2 + - - +
94C VAL 3.2 3.1 + - - -
95C GLU* 3.4 10.2 + - - +
96C THR* 2.5 35.7 + - - -
132C GLU* 3.4 4.3 - - - -
136C LYS* 4.0 10.8 - - - -
267C TYR* 3.8 15.7 - - - -
299C HIS* 3.4 20.2 - + - -
301C THR 4.8 1.6 + - - -
302C ARG* 4.1 16.9 - - + -
303C ARG 4.9 1.7 + - - -
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLY* 3.7 15.1 - - - -
86C TYR 4.4 0.9 - - - -
87C VAL* 3.6 11.6 - - - -
88C ASP* 3.0 21.8 + - - -
90C GLY 3.8 6.1 + - - -
92C TYR* 1.3 72.4 - - - +
94C VAL* 1.3 60.4 + - - +
96C THR* 4.2 0.7 - - - -
97C VAL* 2.8 36.7 + - - +
128C GLY 5.5 0.3 - - - -
129C PHE* 3.4 26.6 + - - +
132C GLU* 2.9 15.3 + - - -
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 4.1 16.6 - - + -
23C LEU 5.7 0.2 - - - +
93C SER* 1.3 76.4 - - - +
95C GLU* 1.3 60.3 + - - +
97C VAL* 3.8 4.2 - - - +
98C THR* 2.5 43.7 + - - +
129C PHE* 4.4 3.1 - - + -
132C GLU* 2.9 25.3 + - + +
133C CYS* 3.8 33.4 - - - +
136C LYS* 4.1 12.1 - - + -
137C TYR* 3.7 31.6 - - + +
142C VAL* 5.2 3.8 - - + -
146C PHE* 5.4 1.3 - - + -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.1 13.1 - - + +
20C CYS* 3.8 42.2 - - - +
21C LYS 4.6 0.7 - - - -
22C GLN* 4.3 20.3 - - - +
62C PHE* 3.9 21.1 - - + -
92C TYR* 3.4 16.2 - - - +
94C VAL* 1.3 75.8 - - - +
96C THR* 1.3 65.7 + - - +
98C THR* 4.0 0.5 - - - -
99C LEU* 3.1 26.7 + - - +
132C GLU* 3.5 1.6 - - - +
136C LYS* 2.9 41.5 + - - +
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 3.8 19.5 - - + -
60C GLY* 3.5 9.0 - - - -
62C PHE* 3.4 29.4 + - - -
65C LEU* 3.8 22.1 - - + +
86C TYR* 3.8 16.4 - - + +
92C TYR 2.5 22.5 + - - -
93C SER 3.8 2.7 - - - -
95C GLU* 1.3 78.1 - - - +
97C VAL* 1.3 57.7 + - - +
99C LEU* 3.8 2.1 - - - +
100C LEU* 3.2 36.6 + - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TYR* 4.1 24.2 - - + -
87C VAL* 3.9 17.5 - - + -
93C SER 2.8 27.9 + - - +
94C VAL 3.8 3.6 - - - +
96C THR* 1.3 72.3 - - - +
98C THR* 1.3 68.2 + - - +
100C LEU* 4.1 5.7 - - + +
101C VAL* 3.1 37.2 + - + +
129C PHE* 4.3 4.5 - - + -
146C PHE* 3.7 30.3 - - + -
150C PHE* 4.1 24.9 - - + -
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Residues in contact with THR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.6 18.4 - - + -
23C LEU* 3.6 35.6 + - + +
28C VAL* 4.9 5.7 - - + +
31C LEU* 3.8 10.6 - - + +
94C VAL* 2.5 30.2 + - - +
97C VAL* 1.3 77.4 - - - +
99C LEU* 1.3 57.0 + - - +
101C VAL* 3.4 3.0 + - - +
102C ALA* 2.8 30.3 + - - +
137C TYR* 5.3 0.2 + - - -
146C PHE* 3.2 25.8 - - + -
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.1 24.7 - - + +
17C LEU* 3.8 25.7 - - + +
18C ASN* 4.1 11.4 - - - +
62C PHE* 4.0 11.2 - - + -
65C LEU* 4.6 5.8 - - + -
66C MET* 3.5 32.8 - - + -
69C PHE* 4.3 10.3 - - + -
74C LYS* 4.9 0.7 - - - +
95C GLU 3.1 18.1 + - - +
96C THR 3.8 3.4 - - - +
98C THR* 1.3 77.2 - - - +
100C LEU* 1.3 57.0 + - - +
102C ALA* 3.2 1.3 + - - +
103C LEU* 2.8 54.8 + - + +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 5.3 2.0 - - + -
65C LEU* 4.0 24.0 - - + -
69C PHE* 4.3 11.0 - - + -
82C PHE* 3.7 40.4 - - + -
86C TYR* 3.8 32.1 - - + -
96C THR* 3.2 25.3 + - + +
97C VAL* 3.7 5.6 + - + +
98C THR 3.4 0.2 - - - -
99C LEU* 1.3 76.9 - - + +
101C VAL* 1.3 62.2 + - + +
103C LEU* 3.6 11.5 + - + +
104C LYS* 3.2 20.1 + - - +
111C ILE* 4.4 4.5 - - + +
113C ILE* 4.1 20.3 - - + +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.8 24.7 - - + +
32C CYS* 5.2 0.7 - - - -
35C ALA* 3.9 24.0 - - + -
97C VAL* 3.1 28.1 + - + +
98C THR 3.7 2.9 - - - +
100C LEU* 1.3 74.6 - - + +
102C ALA* 1.3 60.1 + - - +
104C LYS* 3.1 7.4 + - + +
105C VAL* 3.0 27.9 + - - +
113C ILE* 4.4 13.7 - - + -
146C PHE* 4.3 10.1 - - + -
149C LEU* 3.8 25.6 - - + -
150C PHE* 6.0 0.2 - - + -
153C LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.8 20.6 - - + +
13C TRP* 5.5 1.1 - - + -
14C ILE* 3.8 16.4 - - + +
17C LEU* 4.2 9.0 - - + -
31C LEU* 3.8 18.6 - - + -
98C THR 2.8 18.5 + - - +
99C LEU* 3.2 8.5 + - - +
101C VAL* 1.3 76.6 - - - +
103C LEU* 1.3 58.1 + - - +
105C VAL* 3.6 0.5 + - - +
106C ARG* 3.1 28.9 + - - +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.2 29.6 - - + -
69C PHE* 4.0 26.5 - - + -
74C LYS* 4.3 9.6 - - - -
75C SER* 4.3 24.7 - - - +
99C LEU* 2.8 35.8 + - + +
100C LEU* 3.9 10.1 - - + +
102C ALA* 1.3 73.1 - - - +
104C LYS* 1.3 61.1 + - - +
106C ARG* 4.4 2.0 - - - -
107C TYR* 2.8 45.7 + - + +
111C ILE* 3.9 19.4 - - + +
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Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA* 6.0 3.1 - - + -
38C ILE* 4.6 11.1 - - + +
39C LEU* 4.3 12.1 - - + -
42C GLU* 3.4 36.4 + - - -
100C LEU 3.2 14.5 + - - +
101C VAL* 3.1 10.9 + - + +
103C LEU* 1.3 76.3 - - - +
105C VAL* 1.3 59.8 + - + +
107C TYR 4.6 0.2 - - - -
108C ARG* 2.7 71.3 + - - +
111C ILE* 2.8 30.5 + - + +
112C THR* 4.7 5.2 + - - +
113C ILE* 4.0 28.9 - - + +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 4.0 20.6 - - + -
10C LEU* 3.7 17.7 - - + +
31C LEU* 3.6 18.6 - - + +
34C LYS* 4.1 11.9 - - + -
35C ALA* 3.8 31.6 - - + +
38C ILE* 4.0 19.8 - - + +
101C VAL 3.0 16.2 + - - +
102C ALA 4.0 3.8 - - - +
104C LYS* 1.3 76.8 - - + +
106C ARG* 1.3 63.0 + - - +
108C ARG* 4.3 11.7 + - - +
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Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 3.6 31.9 - - - +
10C LEU* 3.7 18.1 - - + +
11C ASP* 2.9 31.1 + - - +
14C ILE* 3.7 15.7 - - + -
102C ALA 3.1 19.1 + - - +
104C LYS 3.2 0.2 - - - -
105C VAL* 1.3 79.7 - - - +
107C TYR* 1.3 100.1 + - + +
108C ARG* 3.9 0.8 + - - -
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Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 4.5 4.0 + - - -
14C ILE* 4.9 3.3 - - + +
75C SER* 4.2 10.1 - - - -
76C PRO* 3.6 41.7 - - + +
103C LEU* 2.8 35.8 + - + +
104C LYS 3.4 3.8 - - - -
106C ARG* 1.3 122.0 + - + +
108C ARG* 1.3 63.6 + - - +
109C GLU 3.2 2.7 - - - -
110C ARG* 2.9 29.2 + - + -
111C ILE* 3.2 12.7 + - + +
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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