Contacts of the helix formed by residues 97 - 106 (chain Y) in PDB entry 3N5N
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 LEU 97 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95Y ARG* 3.5 32.2 + - + +
96Y ASP* 1.3 85.5 + - - +
98Y PRO* 1.4 66.2 - - + +
99Y TRP* 3.8 32.3 - - + +
100Y ARG* 2.8 57.3 + - + +
101Y ARG* 2.9 13.7 + - - +
128Y VAL* 4.0 24.5 - - + -
132Y ILE* 4.0 11.4 - - + -
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Residues in contact with PRO 98 (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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96Y ASP 4.5 2.5 - - - +
97Y LEU* 1.4 84.2 - - + +
99Y TRP* 1.3 62.1 + - + +
101Y ARG* 3.7 7.5 - - + +
102Y ARG* 2.9 32.1 + - - +
132Y ILE* 3.6 38.6 - - + +
135Y TYR* 3.9 14.3 - - + -
136Y THR* 3.9 23.1 - - - +
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Residues in contact with TRP 99 (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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97Y LEU* 3.8 31.1 - - + +
98Y PRO* 1.3 86.7 - - + +
100Y ARG* 1.3 70.3 + - + +
102Y ARG* 4.0 0.7 - - - +
103Y ALA* 2.9 30.1 + - - +
115Y ALA* 4.7 1.8 - - - +
116Y VAL* 5.7 1.5 - - - +
119Y SER* 3.4 33.2 - - - +
120Y GLU* 5.8 1.8 - - - -
123Y LEU* 3.7 29.6 - - + +
128Y VAL* 4.0 13.2 - - + -
131Y VAL* 3.5 28.0 - - + -
132Y ILE* 3.1 40.8 - - + -
135Y TYR* 3.5 37.3 + + + +
266Y GLN* 4.9 6.1 - - - +
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Residues in contact with ARG 100 (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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90Y TYR* 3.0 28.7 + - - -
94Y LYS* 3.7 7.5 - - + +
95Y ARG* 2.8 31.9 + - - +
96Y ASP* 5.9 0.2 - - - +
97Y LEU* 2.8 33.1 + - + +
99Y TRP* 1.3 88.5 - - + +
101Y ARG* 1.3 68.8 + - - +
103Y ALA* 3.4 3.8 + - - +
104Y GLU* 3.3 30.2 + - - +
266Y GLN* 2.9 42.8 + - - +
270Y GLU* 3.1 38.8 + - - -
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Residues in contact with ARG 101 (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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96Y ASP* 4.3 13.6 + - - +
97Y LEU 2.9 11.7 + - - +
98Y PRO* 3.7 10.5 - - + +
100Y ARG* 1.3 78.1 - - - +
102Y ARG* 1.3 62.5 + - - +
104Y GLU* 3.3 12.5 - - - +
105Y ASP* 3.1 32.5 + - - +
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Residues in contact with ARG 102 (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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98Y PRO* 2.9 16.4 + - - +
99Y TRP 4.0 2.7 - - - +
101Y ARG* 1.3 78.1 - - - +
103Y ALA* 1.3 64.3 + - - +
105Y ASP* 4.6 3.8 - - - +
106Y GLU* 3.0 35.5 + - + +
115Y ALA* 3.5 19.5 - - + -
135Y TYR* 3.3 25.4 - - - -
136Y THR* 5.4 2.4 + - - +
139Y MET* 3.6 45.1 + - - +
140Y GLN* 5.0 1.6 - - - +
143Y PRO* 5.1 7.9 + - - +
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Residues in contact with ALA 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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99Y TRP 2.9 22.3 + - - +
100Y ARG* 3.4 5.3 + - - +
102Y ARG* 1.3 75.1 - - - +
104Y GLU* 1.3 61.0 + - - +
105Y ASP 3.6 0.3 + - - -
106Y GLU 3.9 0.9 + - - -
112Y ARG* 3.1 41.3 + - + +
115Y ALA* 5.1 2.4 - - + +
116Y VAL* 4.0 26.5 - - + +
212Y ILE* 4.3 11.4 - - + +
266Y GLN* 5.6 3.1 - - - +
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Residues in contact with GLU 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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132X ILE* 3.9 26.0 - - + +
133X ASN* 3.9 18.5 - - - +
94Y LYS* 3.9 21.3 + - - -
100Y ARG* 3.3 15.8 + - - +
101Y ARG* 3.3 17.6 - - - +
103Y ALA* 1.3 79.8 - - - +
105Y ASP* 1.3 69.7 + - - +
106Y GLU 4.6 2.0 - - - +
107Y MET* 5.9 1.4 - - - +
112Y ARG* 5.1 4.8 + - - +
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Residues in contact with ASP 105 (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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129X ALA 5.7 0.9 - - - +
132X ILE* 5.9 1.4 - - - +
133X ASN* 4.8 5.0 - - - +
101Y ARG* 3.1 23.6 + - - +
102Y ARG* 3.3 4.0 + - - +
104Y GLU* 1.3 96.5 - - - +
106Y GLU* 1.3 64.2 + - - +
107Y MET* 3.3 16.4 + - - +
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Residues in contact with GLU 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 ARG* 3.0 29.4 + - + +
103Y ALA 3.9 0.6 - - - +
104Y GLU 3.6 0.5 - - - +
105Y ASP* 1.3 77.5 - - - +
107Y MET* 1.3 59.8 + - - +
108Y ASP* 3.2 36.4 + - - +
111Y ARG* 3.3 33.4 + - + +
112Y ARG* 2.8 55.3 + - + +
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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