Contacts of the helix formed by residues 95 - 104 (chain A) in PDB entry 1Q5K
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 ASN 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.8 15.8 - - - +
89A GLN* 3.3 28.2 + - + +
93A PHE 3.8 2.2 + - - -
94A LYS* 1.3 70.2 - - - +
96A ARG* 1.3 65.4 + - - +
97A GLU* 2.9 22.0 + - - +
98A LEU* 2.8 33.4 + - + +
99A GLN* 3.1 25.4 + - - +
128A LEU* 3.4 29.6 - - + +
130A LEU* 5.9 0.4 - - - +
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Residues in contact with ARG 96 (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 PHE* 6.2 3.1 - - + -
94A LYS 3.3 7.0 + - - +
95A ASN* 1.3 71.2 + - - +
97A GLU* 1.3 66.2 + - - +
99A GLN* 3.3 6.5 + - + +
100A ILE* 3.0 41.1 + - + +
180A ARG* 4.2 11.3 - - - +
203A SER 6.2 0.2 - - - -
204A ALA 3.7 13.7 + - - +
205A LYS* 3.8 28.4 - - - +
206A GLN 5.7 0.7 - - - +
291B PHE* 2.8 50.3 - - - -
292B LYS* 5.3 2.8 - - - +
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Residues in contact with GLU 97 (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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85A LYS* 2.5 44.1 + - - +
87A VAL* 5.0 5.7 - - - +
95A ASN* 2.9 16.2 + - - +
96A ARG* 1.3 73.1 - - - +
98A LEU* 1.3 58.7 + - - +
100A ILE* 3.2 4.7 + - - +
101A MET* 2.9 42.3 + - + +
130A LEU* 4.0 19.1 - - + +
132A LEU* 5.9 0.5 - - - +
200A ASP* 4.2 1.0 - - - -
201A PHE* 3.4 38.1 + - + +
202A GLY* 3.5 16.7 - - - +
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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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95A ASN* 2.8 23.3 + - + +
97A GLU* 1.3 77.5 - - - +
99A GLN* 1.3 81.0 + - - +
101A MET* 3.3 3.6 + - - +
102A ARG* 3.0 45.5 + - + +
112A LEU* 3.8 4.9 - - + -
115A PHE* 3.8 39.3 - - + -
117A TYR* 4.0 11.0 - - - +
128A LEU* 4.0 22.4 - - + -
130A LEU* 3.7 25.1 - - + +
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Residues in contact with GLN 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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94A LYS* 4.4 25.4 - - + +
95A ASN 3.1 16.8 + - - +
96A ARG* 3.8 7.6 - - + +
97A GLU 3.3 0.2 - - - -
98A LEU* 1.3 100.1 - - - +
100A ILE* 1.3 64.7 + - + +
102A ARG* 3.6 26.4 + - - +
103A LYS* 3.7 23.3 + - - +
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Residues in contact with ILE 100 (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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96A ARG* 3.0 31.7 + - + +
97A GLU* 3.2 4.7 + - - +
99A GLN* 1.3 79.3 - - + +
101A MET* 1.3 62.8 + - - +
103A LYS* 3.1 20.6 + - + +
104A LEU* 3.3 29.2 + - + +
177A ILE* 4.1 26.5 - - + -
201A PHE* 4.1 17.5 - - + +
204A ALA* 3.5 38.4 - - + +
205A LYS* 4.0 7.4 - - - +
206A GLN 5.0 1.8 - - - +
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Residues in contact with MET 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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46A GLN* 5.6 1.6 - - - +
97A GLU* 2.9 38.7 + - + +
98A LEU* 3.9 5.2 - - - +
100A ILE* 1.3 77.4 - - - +
102A ARG* 1.3 62.8 + - - +
103A LYS 3.0 1.1 + - - -
104A LEU* 3.2 24.6 + - + +
109A ILE* 4.6 3.8 - - + -
110A VAL* 3.3 39.7 - - + +
112A LEU* 4.1 27.2 + - + +
130A LEU* 5.0 4.9 - - + -
132A LEU* 3.8 23.6 - - + -
200A ASP 6.1 0.7 - - - -
201A PHE* 4.0 30.7 - - + -
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Residues in contact with ARG 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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43A THR* 4.4 0.8 - - - +
44A PRO 3.9 15.0 + - - -
45A GLY 3.3 27.6 + - - +
46A GLN* 4.1 13.6 - - - +
47A GLY 4.1 12.5 + - - -
49A ASP* 2.6 39.2 + - - +
98A LEU* 3.0 43.6 + - + +
99A GLN* 4.0 21.8 + - - +
100A ILE 3.3 0.2 - - - -
101A MET* 1.3 75.4 - - - +
103A LYS* 1.3 60.9 + - + +
104A LEU 4.8 0.7 - - - -
112A LEU* 3.8 7.2 - - + -
115A PHE* 3.6 27.8 - - - -
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Residues in contact with LYS 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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46A GLN* 6.1 0.2 - - - -
99A GLN* 3.7 19.5 - - - +
100A ILE* 3.1 12.6 + - - +
101A MET 3.0 0.8 - - - -
102A ARG* 1.3 81.2 - - + +
104A LEU* 1.3 66.0 + - + +
105A ASP* 3.8 3.5 + - - +
171A TYR* 3.8 6.9 + - - -
175A PHE* 5.4 9.8 - - + -
177A ILE* 5.4 10.6 - - + +
206A GLN* 4.8 11.3 + - - -
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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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46A GLN* 4.0 14.4 + - - +
100A ILE* 3.3 26.2 - - + +
101A MET* 3.2 21.5 + - + +
103A LYS* 1.3 82.2 - - + +
105A ASP* 1.3 62.2 + - - +
109A ILE* 4.2 16.8 - - + -
110A VAL 6.0 0.2 - - - +
111A ARG* 5.8 2.4 - - - +
112A LEU 5.9 1.2 + - - -
171A TYR* 3.7 21.5 - - + -
172A ILE* 4.2 13.7 - - + -
175A PHE* 5.1 6.5 - - + -
177A ILE* 4.3 18.2 - - + -
201A PHE* 3.6 39.5 - - + -
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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