Contacts of the helix formed by residues 101 - 117 (chain Y) in PDB entry 6CP3
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 PHE 101 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Y LEU* 5.3 11.2 - - + -
43Y VAL* 4.3 28.9 - - + -
44Y GLU* 5.0 9.0 - - - -
47Y VAL* 5.0 16.2 - - + -
58Y LEU* 5.2 17.3 - - + -
74Y ILE* 5.9 4.0 - - + -
88Y LEU* 6.0 6.7 - - + -
89Y LEU* 4.2 27.1 - - + -
92Y LEU* 6.0 4.0 - - + -
97Y ARG 4.8 0.4 - - - +
98Y LEU* 2.8 32.8 - - + +
99Y GLY 2.9 9.2 + - - +
100Y CYS* 1.3 71.9 - - - +
102Y GLU* 1.3 62.4 + - + +
103Y LYS 3.0 6.4 - - - +
104Y ILE* 3.0 28.5 + - + +
105Y ALA* 3.0 14.5 + - + -
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Residues in contact with GLU 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Y GLU* 3.2 35.0 - - - +
47Y VAL* 6.5 0.4 - - + -
58Y LEU* 6.1 6.0 - - + +
99Y GLY 4.8 3.8 + - - +
101Y PHE* 1.3 80.4 - - + +
103Y LYS* 1.3 72.2 + - - +
105Y ALA* 2.9 7.2 + - - +
106Y SER* 2.8 30.3 + - - -
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Residues in contact with LYS 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLU* 5.3 6.3 + - - -
15Y VAL* 4.4 20.9 + - - +
16Y GLU* 5.5 7.8 - - + +
100Y CYS* 4.6 19.7 - - + +
101Y PHE 3.0 0.8 - - - +
102Y GLU* 1.3 91.2 - - - +
104Y ILE* 1.3 66.1 + - + +
106Y SER* 3.2 8.9 + - - +
107Y ASP* 2.9 45.6 + - - +
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Residues in contact with ILE 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Y GLU* 3.9 19.1 - - + +
17Y GLY* 5.5 0.9 - - - -
19Y TYR* 4.1 30.1 - - + -
20Y ALA* 3.8 27.8 - - + +
23Y LEU* 5.7 5.6 - - + -
40Y LEU* 6.4 0.9 - - + -
88Y LEU* 5.9 6.7 - - + -
92Y LEU* 5.0 7.4 - - + -
97Y ARG* 6.2 0.2 - - + -
100Y CYS 3.0 26.2 - - - +
101Y PHE* 3.0 20.3 + - + +
103Y LYS* 1.3 81.3 - - + +
105Y ALA* 1.3 55.1 + - - +
107Y ASP* 3.8 5.6 - - - +
108Y PHE* 2.8 30.2 + - + +
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Residues in contact with ALA 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y PHE* 5.7 0.3 - - - -
40Y LEU* 5.1 20.4 - - + +
41Y GLN* 5.6 2.6 + - - -
44Y GLU* 3.9 22.4 - - + +
101Y PHE* 3.0 13.8 + - + +
102Y GLU* 2.9 22.5 + - - +
104Y ILE* 1.3 77.7 - - - +
106Y SER* 1.3 55.0 - - - +
108Y PHE* 3.8 4.8 - - - +
109Y GLY* 2.9 25.3 + - - -
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Residues in contact with SER 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y GLU* 2.8 15.4 + - - -
103Y LYS* 3.2 12.1 + - - -
105Y ALA* 1.3 75.7 - - - +
107Y ASP* 1.3 59.1 + - - +
109Y GLY* 3.2 3.0 + - - -
110Y VAL* 2.9 33.7 + - - +
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Residues in contact with ASP 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Y LEU* 5.8 4.7 - - + -
15Y VAL 5.2 0.5 - - - +
17Y GLY* 4.5 15.5 - - - -
20Y ALA* 4.8 9.6 - - + -
103Y LYS* 2.9 42.8 + - - +
104Y ILE* 3.8 6.7 - - - +
105Y ALA 3.2 0.2 - - - -
106Y SER* 1.3 75.2 - - - +
108Y PHE* 1.3 64.9 + - - +
110Y VAL* 3.1 15.3 + - - +
111Y LEU* 2.9 23.2 + - - +
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Residues in contact with PHE 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y ALA* 4.6 15.1 - - + +
23Y LEU* 4.3 16.4 - - + -
24Y TYR* 3.9 45.8 - + + -
27Y ALA* 6.0 1.6 - - + -
33Y ILE* 4.2 17.9 - - + -
36Y ALA* 4.4 8.5 - - + -
37Y PHE* 3.8 33.9 - + + -
40Y LEU* 2.9 35.7 - - + -
104Y ILE* 2.8 22.4 + - + +
105Y ALA 3.9 1.1 - - - +
107Y ASP* 1.3 72.7 - - - +
109Y GLY* 1.3 58.1 + - - +
111Y LEU* 3.3 6.6 + - + +
112Y ASN* 2.8 33.7 + - + +
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Residues in contact with GLY 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y PHE* 3.5 23.9 - - - -
41Y GLN* 5.4 1.6 - - - -
105Y ALA 2.9 14.6 + - - -
106Y SER* 3.5 4.9 - - - -
107Y ASP 3.1 0.4 - - - -
108Y PHE* 1.3 78.0 - - - +
110Y VAL* 1.3 48.7 + - - +
112Y ASN* 3.7 0.7 - - - +
113Y ASP* 2.7 42.6 + - - +
120Y LYS* 5.8 0.2 - - - -
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Residues in contact with VAL 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y VAL* 5.4 7.2 - - + -
106Y SER* 2.9 21.6 + - - +
107Y ASP* 3.1 17.7 + - - +
109Y GLY* 1.3 74.5 - - - +
111Y LEU* 1.3 60.2 + - + +
113Y ASP* 2.3 25.4 - - - +
114Y ALA* 2.9 17.9 + - + +
120Y LYS* 5.0 10.1 - - - +
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Residues in contact with LEU 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y PRO* 5.8 1.1 - - + -
9Y PRO* 3.2 32.7 - - + +
10Y VAL* 3.2 28.3 - - + +
20Y ALA* 5.3 3.1 - - + +
21Y THR* 5.2 10.3 - - + +
24Y TYR* 3.4 52.1 - - + -
107Y ASP 2.9 15.4 + - - +
108Y PHE* 3.7 9.4 - - + +
110Y VAL* 1.3 78.6 - - + +
112Y ASN* 1.3 59.4 + - - +
114Y ALA* 3.2 5.1 + - + +
115Y HIS* 2.9 26.0 + - - +
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Residues in contact with ASN 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y TYR* 5.6 4.2 - - - -
33Y ILE* 4.2 22.2 + - - +
34Y ASP* 5.4 2.5 - - - +
37Y PHE* 2.7 56.6 - - + +
108Y PHE* 2.8 25.2 + - + +
109Y GLY 3.7 1.6 - - - +
111Y LEU* 1.3 76.5 - - - +
113Y ASP* 1.3 58.8 + - - +
115Y HIS* 2.8 22.7 + - - +
116Y ASN* 2.9 26.4 + - - +
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Residues in contact with ASP 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y PHE* 6.0 2.9 - - + -
109Y GLY 2.7 16.8 + - - +
110Y VAL* 2.3 37.3 - - - +
112Y ASN* 1.3 72.0 - - - +
114Y ALA* 1.3 58.3 + - - +
116Y ASN* 4.0 11.7 - - - +
117Y GLY 2.8 4.2 + - - -
118Y LEU* 2.7 59.0 + - + +
120Y LYS* 2.6 38.3 + - - -
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Residues in contact with ALA 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y PRO* 5.7 6.1 - - + -
10Y VAL* 4.5 18.2 - - + -
110Y VAL* 2.9 16.0 + - + +
111Y LEU* 3.3 9.9 - - + +
113Y ASP* 1.3 81.1 + - - +
115Y HIS* 1.3 61.4 + - - +
117Y GLY* 2.8 20.4 + - - +
118Y LEU 4.8 2.5 - - - +
119Y LEU* 5.5 3.9 - - + +
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Residues in contact with HIS 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y PRO* 5.1 10.4 - - + +
24Y TYR* 4.0 26.2 + - + +
33Y ILE* 4.0 26.1 - - + +
111Y LEU 2.9 11.7 + - - +
112Y ASN* 2.8 17.6 + - - +
114Y ALA* 1.3 77.8 - - - +
116Y ASN* 1.3 62.5 + - - +
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Residues in contact with ASN 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y ILE* 5.8 0.5 - - - +
112Y ASN* 2.9 28.2 + - - +
113Y ASP* 3.8 9.2 - - - +
115Y HIS* 1.3 79.6 + - - +
117Y GLY* 1.3 60.8 + - - +
118Y LEU* 3.5 26.0 - - + +
150Y GLY 4.3 5.0 - - - +
151Y LYS* 4.0 13.5 - - - +
152Y SER 4.4 1.7 + - - -
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Residues in contact with GLY 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Y ASP 2.8 3.3 + - - -
114Y ALA 2.8 18.5 + - - -
116Y ASN* 1.3 79.0 - - - +
118Y LEU* 1.3 59.8 + - - +
119Y LEU* 2.8 31.2 + - - +
151Y LYS* 3.3 25.1 - - - +
152Y SER 3.5 5.5 + - - -
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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
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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