Contacts of the helix formed by residues 95 - 102 (chain B) in PDB entry 1Q4L
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL* 3.8 18.0 - - - +
88B LEU 5.1 0.4 + - - -
89B GLN* 3.1 33.5 + - - +
93B PHE 3.6 3.2 + - - -
94B LYS* 1.3 70.1 - - - +
96B ARG* 1.3 64.0 + - - +
97B GLU* 2.9 35.6 + - - +
98B LEU* 3.1 14.0 + - + +
99B GLN* 3.2 26.3 + - - +
128B LEU* 3.5 26.2 - - + +
130B LEU* 5.9 0.6 - - - +
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS 3.3 6.2 + - - +
95B ASN* 1.3 72.1 + - - +
97B GLU* 1.3 65.9 + - - +
99B GLN* 3.4 6.5 + - + +
100B ILE* 3.1 34.5 + - + +
180B ARG* 4.0 13.3 - - - +
203B SER 5.8 0.4 - - - -
204B ALA 3.5 19.2 + - - -
205B LYS* 3.2 44.2 - - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 5.6 1.6 - - - -
85B LYS* 2.7 43.0 + - - +
87B VAL* 5.0 4.3 - - - +
95B ASN* 2.9 15.2 + - - +
96B ARG* 1.3 73.2 - - - +
98B LEU* 1.3 57.9 + - - +
100B ILE* 3.3 4.5 + - - +
101B MET* 2.9 48.9 + - + +
130B LEU* 4.0 16.9 - - + +
200B ASP* 4.4 0.9 - - - -
201B PHE* 3.2 30.7 + - + +
202B GLY* 3.2 21.5 + - - -
204B ALA 6.1 0.2 - - - -
452B 679 4.7 0.3 - - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN* 3.1 23.3 + - + +
97B GLU* 1.3 78.2 - - - +
99B GLN* 1.3 76.0 + - - +
101B MET* 3.3 3.5 + - - +
102B ARG* 3.0 41.6 + - + +
112B LEU* 3.5 25.1 - - + -
115B PHE* 3.7 44.4 - - + -
117B TYR* 4.3 8.7 - - - +
128B LEU* 4.2 18.8 - - + -
130B LEU* 4.3 8.0 - - + +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS* 4.6 28.3 - - + +
95B ASN 3.2 19.2 + - - +
96B ARG* 3.9 7.9 - - + +
97B GLU 3.3 0.2 - - - -
98B LEU* 1.3 100.9 - - - +
100B ILE* 1.3 63.6 + - + +
102B ARG* 3.8 20.9 + - - +
103B LYS* 3.8 18.2 + - - +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ARG* 3.1 28.6 + - + +
97B GLU* 3.8 5.4 - - - +
99B GLN* 1.3 78.7 - - + +
101B MET* 1.3 64.4 + - - +
103B LYS* 3.3 16.3 + - - +
104B LEU* 3.2 29.1 - - + +
177B ILE* 4.0 31.0 - - + -
201B PHE* 4.1 19.3 - - + -
204B ALA* 3.4 37.0 - - + +
205B LYS* 3.9 9.9 - - - +
206B GLN* 4.6 4.3 - - + +
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 3.5 9.5 + - - -
97B GLU* 2.9 36.1 + - + +
98B LEU* 3.9 1.8 - - - +
100B ILE* 1.3 73.4 - - - +
102B ARG* 1.3 57.0 + - - +
103B LYS 2.9 10.8 + - - -
104B LEU* 3.0 28.9 + - + +
109B ILE* 4.5 0.4 - - + -
110B VAL* 4.0 19.5 - - + +
112B LEU* 3.5 28.0 + - + +
130B LEU* 5.1 4.3 - - + -
132B LEU* 4.2 25.6 - - - -
201B PHE* 3.5 44.4 - - + -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 4.3 2.0 - - - +
44B PRO 3.7 15.0 + - - -
45B GLY 3.4 27.3 + - - +
46B GLN* 3.5 17.4 + - - +
47B GLY 3.9 18.2 + - - +
49B ASP* 3.1 31.3 + - - +
98B LEU* 3.0 39.3 + - + +
99B GLN* 4.2 19.3 + - - +
100B ILE 3.5 0.2 - - - -
101B MET* 1.3 74.4 - - - +
103B LYS* 1.3 56.3 + - + +
104B LEU 3.6 0.4 - - - -
112B LEU* 4.0 5.6 - - + -
115B PHE* 3.6 30.2 - - + -
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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