Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 2H4Q
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A SER* 4.7 4.3 + - - +
3A GLN* 5.2 3.0 + - - +
91A ALA* 4.2 2.0 - - - +
92A GLU* 1.3 93.9 - - - +
94A ILE* 1.3 63.8 + - - +
95A HIS* 3.1 28.7 + - - +
96A SER* 3.0 36.6 + - - -
97A GLY 3.8 1.9 + - - -
139A TYR* 3.2 25.1 + - - -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 4.6 4.7 - - + +
4A VAL* 3.4 29.2 - - + +
7A SER* 4.6 1.6 - - - +
40A ALA* 5.5 0.2 - - + -
43A TYR* 3.9 29.8 - - + -
59A HIS 4.9 0.2 - - - +
60A PHE* 3.6 43.7 - - + +
91A ALA* 3.7 27.8 + - + +
92A GLU 4.1 0.4 - - - -
93A ASN* 1.3 73.3 - - - +
95A HIS* 1.3 80.8 + - + +
97A GLY 3.2 11.5 + - - +
98A PHE* 3.2 26.7 + - + -
140A TYR* 5.0 0.2 - - - +
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Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.5 20.9 - - - -
43A TYR* 3.8 22.4 + + - -
44A LEU* 3.5 40.8 - - + +
93A ASN* 3.0 15.4 + - - +
94A ILE* 1.3 85.1 - - + +
96A SER* 1.3 55.9 + - - +
98A PHE* 3.5 2.2 + - - +
99A LYS* 3.0 21.3 + - - +
139A TYR* 3.3 38.4 - + + +
140A TYR* 2.7 31.7 + - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3A LEU* 3.8 19.6 - - - +
0A SER* 3.8 14.5 + - - -
93A ASN* 3.0 32.8 + - - -
95A HIS* 1.3 76.2 - - - +
97A GLY* 1.3 60.0 + - - +
99A LYS* 3.2 6.6 + - - +
100A GLU* 2.9 32.1 + - - +
139A TYR* 3.8 12.0 - - - -
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Residues in contact with GLY 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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0A SER* 3.6 36.0 - - - -
1A MET* 4.0 3.5 - - - +
4A VAL* 3.6 11.2 - - - -
93A ASN 3.8 2.4 + - - -
94A ILE 3.2 4.8 + - - -
96A SER* 1.3 77.5 - - - +
98A PHE* 1.3 56.6 + - - +
100A GLU* 3.4 1.0 + - - +
101A LEU* 2.9 34.5 + - - +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.6 25.3 - - + +
8A ILE* 4.3 5.6 - - + -
33A TRP* 3.8 22.4 - + - -
36A SER* 3.5 23.3 - - - -
37A SER* 3.5 34.8 - - - -
40A ALA* 3.7 17.0 - - + -
60A PHE* 3.9 6.5 - + - -
94A ILE* 3.2 40.3 + - + -
95A HIS 3.7 4.7 - - - +
96A SER 3.3 0.2 - - - -
97A GLY* 1.3 72.7 - - - +
99A LYS* 1.3 61.4 + - - +
102A LEU* 2.9 32.1 + - - +
139A TYR 4.2 1.6 - - - -
140A TYR* 3.6 36.3 - + + +
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Residues in contact with LYS 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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95A HIS 3.0 15.4 + - - +
96A SER* 3.3 10.8 - - - +
98A PHE* 1.3 76.7 - - - +
100A GLU* 1.3 78.0 + - - +
102A LEU* 3.3 4.7 + - - +
103A THR* 2.9 40.2 + - - +
138A LYS* 3.5 38.1 - - + +
139A TYR* 3.3 32.5 + - + +
141A LYS* 6.5 0.4 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-7A TRP* 5.9 0.3 - - - -
-3A LEU* 3.9 46.3 - - + +
0A SER* 5.4 0.2 - - - -
1A MET* 3.5 30.2 - - + +
96A SER* 2.9 20.6 + - - +
99A LYS* 1.3 101.8 + - - +
101A LEU* 1.3 60.6 + - - +
103A THR* 3.5 12.4 + - - +
104A ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.9 23.6 - - + +
4A VAL* 3.6 37.9 - - + -
5A SER* 3.8 13.2 - - - +
33A TRP* 3.8 20.9 - - + -
97A GLY 2.9 16.9 + - - +
100A GLU* 1.3 74.4 - - - +
102A LEU* 1.3 59.9 + - - +
104A ALA* 3.2 5.6 + - + +
105A PHE* 2.9 45.6 + - + -
396B SER* 3.6 32.3 - - - +
398B THR* 3.7 9.9 - - + +
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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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33A TRP* 3.9 16.2 - - + -
98A PHE 2.9 19.8 + - - +
99A LYS* 3.5 4.7 - - + +
101A LEU* 1.3 75.1 - - - +
103A THR* 1.3 58.7 + - - +
105A PHE* 3.3 3.2 + - + +
106A ASN* 2.9 58.7 + - - +
116A SER* 3.6 33.2 - - - +
117A ALA* 4.7 1.3 - - - +
118A ASN* 4.1 10.3 - - - +
139A TYR 4.4 3.6 - - - +
140A TYR* 3.6 35.9 - - + +
141A LYS* 4.0 20.0 - - + -
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Residues in contact with THR 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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99A LYS* 2.9 29.3 + - - +
100A GLU* 3.7 15.5 + - - +
102A LEU* 1.3 77.1 - - - +
104A ALA* 1.3 61.5 + - - +
106A ASN* 3.4 5.5 + - - +
107A LYS* 3.1 43.8 + - - +
141A LYS* 5.7 5.2 - - - +
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Residues in contact with ALA 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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1A MET* 5.2 7.2 - - - -
100A GLU 3.0 14.9 + - - +
101A LEU* 3.5 11.7 - - + +
103A THR* 1.3 76.7 - - - +
105A PHE* 1.3 69.2 + - + +
107A LYS* 3.3 17.6 + - - +
109A ARG* 3.2 15.4 + - - -
393B HIS* 4.8 15.8 + - + +
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.7 50.0 - + - -
101A LEU* 2.9 34.4 + - + +
102A LEU* 3.8 3.6 - - - +
104A ALA* 1.3 76.4 - - + +
106A ASN* 1.3 63.0 + - - +
107A LYS 3.3 0.4 - - - -
109A ARG* 3.0 24.6 + - - -
114A LEU* 3.1 33.3 - - + +
116A SER* 5.3 7.0 - - - +
193A ILE* 5.5 2.2 - - + -
393B HIS* 3.5 44.2 - + + -
396B SER* 4.1 1.6 - - - -
398B THR* 4.1 14.8 - - + -
400B LEU* 3.8 21.8 - - + -
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Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.9 35.4 + - - +
103A THR* 3.7 5.4 - - - +
105A PHE* 1.3 73.9 - - - +
107A LYS* 1.3 66.0 + - - +
108A PRO* 3.3 6.6 - - - +
109A ARG* 4.6 0.7 - - - -
114A LEU 4.3 4.3 - - - -
115A ARG* 3.2 9.7 - - - +
116A SER* 2.9 46.5 + - - -
141A LYS* 4.9 9.3 - - + +
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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