Contacts of the helix formed by residues 97 - 109 (chain A) in PDB entry 1S3Y
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.6 19.4 - - - +
95A ALA* 3.3 1.6 + - - +
96A LYS* 1.3 81.8 - - - +
98A LEU* 1.3 59.4 + - - +
99A ASP* 3.2 7.1 + - - +
100A HIS* 3.0 35.4 + - - +
101A ALA 3.0 24.8 + - - -
207A NAP 4.2 8.1 - - - -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.0 18.4 - - + -
56A LEU* 3.9 29.6 - - + +
80A ILE* 4.4 9.5 - - + +
97A SER* 1.3 74.6 - - - +
99A ASP* 1.3 63.4 + - - +
101A ALA* 3.5 3.1 + - - +
102A LEU* 3.3 28.2 + - + +
122A VAL* 4.7 6.5 - - + -
128A LEU* 3.9 24.4 - - + +
131A ALA* 4.0 13.7 - - + +
132A ALA* 3.8 28.9 - - - +
135A HIS* 3.8 23.8 - - - +
207A NAP 5.1 3.6 + - - -
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 4.4 9.1 - - - +
97A SER* 3.2 6.0 + - - +
98A LEU* 1.3 79.2 - - - +
100A HIS* 1.3 64.9 + - + +
102A LEU* 3.3 12.0 + - - +
103A GLU* 3.2 23.9 + - - +
135A HIS* 2.9 35.6 + - - -
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 4.2 3.1 - - + +
96A LYS* 3.5 45.6 + - + +
97A SER* 3.0 42.4 + - - +
99A ASP* 1.3 78.7 - - + +
101A ALA* 1.3 59.3 + - - +
103A GLU* 2.6 46.3 + - - +
104A LEU* 3.2 10.0 + - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 4.1 12.3 - - + -
78A VAL* 4.0 14.5 - - + +
80A ILE* 3.5 19.1 - - + -
95A ALA* 3.5 23.7 - - + +
97A SER 3.0 7.4 + - - +
98A LEU* 3.8 5.6 - - - +
100A HIS* 1.3 73.6 - - - +
102A LEU* 1.3 66.9 + - - +
104A LEU* 3.2 7.0 + - - +
105A LEU* 2.9 29.2 + - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 4.1 11.7 - - - +
3A GLN* 6.3 0.4 - - + -
7A LEU* 3.8 31.4 - - + -
56A LEU* 5.1 3.8 - - + -
98A LEU* 3.3 17.6 + - + +
99A ASP* 3.3 23.7 + - - +
101A ALA* 1.3 80.5 - - + +
103A GLU* 1.3 59.6 + - - +
105A LEU* 3.0 18.1 + - + +
106A TYR* 2.8 61.2 + - + +
120A ILE* 4.7 9.2 - - + -
135A HIS* 4.1 16.6 - - + +
137A LYS* 5.7 2.2 - - + -
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 3.0 29.3 + - - +
99A ASP 3.2 5.6 + - - +
100A HIS* 2.6 58.9 + - - +
102A LEU* 1.3 77.9 - - - +
104A LEU* 1.3 62.7 + - + +
106A TYR* 3.4 5.1 + - - +
107A ARG* 3.1 27.1 + - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 5.8 1.3 - - + -
93A HIS* 4.4 27.6 - - + +
94A SER 4.0 21.5 - - - +
95A ALA* 5.3 4.5 - - + -
100A HIS 3.2 9.6 + - - +
101A ALA* 3.5 8.5 - - - +
102A LEU 3.2 0.6 - - - -
103A GLU* 1.3 84.3 - - + +
105A LEU* 1.3 53.1 + - + +
107A ARG* 3.2 29.1 + - - +
108A THR* 2.8 61.8 + - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.0 26.7 - - + -
56A LEU* 4.2 12.8 - - + -
76A ILE* 4.3 1.3 - - + -
78A VAL* 3.9 23.8 - - + -
93A HIS* 4.6 2.9 - - + -
101A ALA 2.9 24.2 + - - +
102A LEU* 3.4 15.3 - - + +
104A LEU* 1.3 78.6 - - + +
106A TYR* 1.3 60.8 + - + +
108A THR* 4.8 0.4 - - - -
109A TYR* 3.0 59.8 + - + +
117A ILE* 3.6 15.7 - - + +
120A ILE* 4.2 15.9 - - + -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.6 4.0 - - - +
2A ASN* 2.9 34.2 + - - +
3A GLN* 4.7 0.3 - - - -
4A GLN* 3.5 32.3 - - + +
5A LYS* 3.8 39.1 + - + +
102A LEU* 2.8 53.8 + - + +
103A GLU* 3.4 8.5 + - - +
105A LEU* 1.3 80.1 - - + +
107A ARG* 1.3 60.5 + - - +
109A TYR 4.2 3.1 - - - -
110A GLY* 3.7 18.9 + - - -
117A ILE* 4.8 13.5 - - + -
120A ILE* 5.0 4.6 - - + +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.1 19.3 + - - +
104A LEU* 3.7 30.3 - - - +
106A TYR* 1.3 79.0 - - - +
108A THR* 1.3 63.9 + - - +
109A TYR 3.3 0.7 - - - -
110A GLY* 4.1 4.5 + - - -
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A HIS* 4.3 22.5 - - + -
104A LEU* 2.8 41.3 + - - +
107A ARG* 1.3 80.4 + - - +
109A TYR* 1.3 79.8 + - + +
110A GLY 3.7 0.9 - - - -
113A SER* 3.8 9.7 - - - -
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.6 33.6 - - + +
91A GLY 5.1 2.1 + - - -
93A HIS* 2.6 35.8 + + - -
105A LEU* 3.0 42.5 + - + +
106A TYR* 4.1 2.3 - - - +
108A THR* 1.3 94.0 - - + +
110A GLY* 1.3 64.5 + - - +
113A SER* 3.2 9.9 + - - -
115A VAL* 3.6 38.1 - - + +
116A GLN* 4.1 9.2 - - - +
117A ILE* 4.0 19.5 + - + +
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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