Contacts of the helix formed by residues 92 - 107 (chain A) in PDB entry 1H13
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 LYS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASN* 5.6 6.5 + - - +
37A PHE* 3.6 40.7 - - + +
38A ASP* 3.7 20.6 + - - -
87A ALA* 2.9 14.0 + - - +
90A LEU* 3.6 34.5 - - + +
91A ASN* 1.3 75.2 - - - +
93A GLN* 1.3 63.4 + - - +
94A GLU 3.6 1.8 - - - -
95A GLU* 3.5 20.0 + - - +
96A PHE* 3.1 22.2 + - - +
160A TRP* 4.0 2.6 - - - -
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Residues in contact with GLN 93 (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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91A ASN 3.5 4.9 + - - +
92A LYS* 1.3 70.5 - - - +
94A GLU* 1.3 63.8 + - + +
95A GLU* 4.2 0.4 + - - -
96A PHE* 3.2 1.7 + - - +
97A ASP* 2.8 45.1 + - - +
160A TRP* 3.7 55.3 + - + +
168A TYR* 3.0 20.4 + - - +
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Residues in contact with GLU 94 (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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50A TYR* 5.5 0.2 - - - +
92A LYS 3.6 0.4 - - - -
93A GLN* 1.3 78.4 - - + +
95A GLU* 1.3 65.9 + - - +
97A ASP* 3.2 13.4 + - - +
98A ASN* 2.8 51.4 + - - +
101A ARG* 5.4 2.3 + - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.0 16.7 - - + -
41A PHE* 3.8 37.0 - - + +
50A TYR* 3.5 24.2 - - + +
87A ALA* 4.3 2.0 - - + -
92A LYS* 3.5 32.0 - - - +
93A GLN 3.2 0.4 + - - -
94A GLU* 1.3 82.9 + - - +
96A PHE* 1.3 61.9 + - - +
98A ASN* 3.9 1.2 - - - +
99A LEU* 3.1 29.9 + - - +
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Residues in contact with PHE 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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84A MET* 3.3 63.5 - - + +
87A ALA* 3.9 7.3 - - + +
88A VAL* 3.9 10.3 - - + -
92A LYS 3.1 14.9 + - - +
93A GLN 3.4 7.6 - - - +
95A GLU* 1.3 77.4 - - - +
97A ASP* 1.3 70.7 + - - +
99A LEU* 3.2 6.3 + - - +
100A TRP* 2.8 29.6 + - + +
152A ALA* 3.7 24.0 - - + -
153A LEU* 3.9 7.4 - - + -
156A ALA* 3.6 14.6 - - + -
160A TRP* 3.5 19.1 - + + -
168A TYR* 3.7 21.8 - + - -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLN* 2.8 34.8 + - - +
94A GLU* 3.7 14.3 - - - +
96A PHE* 1.3 77.9 - - - +
98A ASN* 1.3 57.4 + - - +
100A TRP* 4.6 0.2 - - - -
101A ARG* 2.8 44.5 + - - +
165A GLU* 4.3 8.3 - - - +
166A PHE* 3.6 22.5 - - + -
168A TYR* 2.5 40.7 + - - -
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Residues in contact with ASN 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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50A TYR* 3.1 21.9 + - - +
59A TYR* 3.0 25.4 + - - +
61A ALA* 3.4 2.6 - - - +
62A HIS* 3.0 37.2 + - + +
94A GLU* 2.8 33.2 + - - +
95A GLU 3.9 1.1 - - - +
97A ASP* 1.3 77.6 - - - +
99A LEU* 1.3 61.4 + - - +
101A ARG* 3.0 27.8 + - - +
102A PHE 3.4 12.6 + - - -
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Residues in contact with LEU 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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41A PHE* 4.1 13.7 - - + -
50A TYR* 3.9 14.1 - - + -
62A HIS 3.5 18.2 - - - +
63A TYR* 3.7 19.3 - - - -
64A ILE* 3.9 5.4 - - + +
80A GLN* 2.9 32.3 - - - +
83A GLY* 3.6 37.2 - - - +
84A MET* 3.6 15.5 - - + +
87A ALA* 5.5 0.2 - - + -
95A GLU 3.1 22.1 + - - +
96A PHE 3.6 3.1 - - - +
98A ASN* 1.3 74.8 - - - +
100A TRP* 1.3 64.1 + - - +
102A PHE 3.2 1.4 + - - -
103A ALA* 3.0 14.0 + - - +
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Residues in contact with TRP 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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84A MET* 3.6 25.3 - - + -
96A PHE* 2.8 24.3 + + + +
97A ASP* 4.0 2.5 - - - +
99A LEU* 1.3 73.1 - - - +
101A ARG* 1.3 67.1 + - - +
103A ALA* 3.1 19.8 + - + -
104A LYS* 2.9 41.4 + - + +
122A TYR* 3.4 25.6 - + - -
149A PHE* 4.2 6.5 - + - -
153A LEU* 3.6 34.3 - - + +
166A PHE* 3.6 35.2 - + - -
171A ASP* 2.9 33.3 + - + -
175A MET* 3.6 24.0 - - + -
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Residues in contact with ARG 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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59A TYR* 3.5 14.3 + - - -
60A LYS 3.2 28.2 + - - +
61A ALA* 3.8 4.4 - - + +
94A GLU* 5.4 2.4 + - - -
97A ASP* 2.8 29.9 + - - +
98A ASN* 3.0 36.9 + - - +
99A LEU 3.3 0.2 - - - -
100A TRP* 1.3 76.4 - - - +
102A PHE* 1.3 62.3 + - - +
104A LYS* 4.0 2.2 - - - +
105A ALA* 3.1 29.9 + - + +
165A GLU* 2.8 42.1 + - - +
166A PHE* 3.8 14.6 - - + -
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Residues in contact with PHE 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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53A TYR* 4.1 17.9 - + + -
61A ALA* 3.5 14.2 - - + +
62A HIS 3.0 30.5 - - - +
63A TYR* 3.8 30.5 - + + -
75A ILE* 3.9 24.5 - - + -
80A GLN* 3.6 15.0 - - - -
98A ASN 3.4 1.4 + - - -
99A LEU 3.2 3.5 + - - +
100A TRP 3.2 0.2 - - - -
101A ARG* 1.3 77.5 - - - +
103A ALA* 1.3 63.0 + - - +
106A TYR* 2.8 53.2 + + + +
107A GLN* 4.2 4.5 - - + -
126A LEU* 3.9 18.6 - - + -
134A VAL* 4.0 15.3 - - + -
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Residues in contact with ALA 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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80A GLN* 4.3 0.9 - - + -
99A LEU 3.0 13.6 + - - +
100A TRP* 3.1 25.3 + - + +
102A PHE* 1.3 77.4 - - - +
104A LYS* 1.3 60.0 + - - +
107A GLN* 2.9 50.1 + - - +
108A LYS 3.0 9.9 + - - -
122A TYR* 3.4 5.8 - - + -
149A PHE* 3.8 16.8 - - + -
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Residues in contact with LYS 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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100A TRP* 2.9 44.0 + - + +
101A ARG* 4.2 3.6 - - - +
103A ALA* 1.3 78.5 - - - +
105A ALA* 1.3 60.1 + - - +
108A LYS* 3.5 28.1 - - + +
122A TYR* 4.1 13.7 - - - +
166A PHE* 4.5 15.1 - - + -
171A ASP* 2.8 31.3 + - - -
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Residues in contact with ALA 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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101A ARG* 3.1 21.6 + - + +
104A LYS* 1.3 79.4 - - - +
106A TYR* 1.3 88.7 + - + +
108A LYS 4.9 4.9 - - - +
136A LYS* 5.1 2.6 + - - -
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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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53A TYR* 3.8 21.8 - + - -
55A GLU* 4.0 10.9 + - - -
60A LYS* 3.6 34.5 - - + +
61A ALA* 4.6 3.1 - - + -
102A PHE* 2.8 47.3 + + + +
105A ALA* 1.3 99.1 - - + +
107A GLN* 1.3 58.9 + - - +
108A LYS 3.6 0.4 - - - -
126A LEU* 3.5 25.8 - - + +
134A VAL* 3.7 24.0 - - + -
136A LYS* 3.0 26.3 + - - +
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Residues in contact with GLN 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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75A ILE* 4.1 16.0 + - - +
76A ARG* 3.5 32.5 + - - +
77A THR* 3.7 11.0 - - + +
80A GLN* 3.5 15.9 - - - +
102A PHE* 3.6 6.5 + - + -
103A ALA* 2.9 36.2 + - - +
106A TYR* 1.3 76.0 - - - +
108A LYS* 1.3 64.7 + - - +
109A ASN 3.3 0.7 + - - -
122A TYR* 3.8 9.2 - - + -
123A ALA* 2.8 38.9 + - - +
126A LEU* 3.7 24.5 - - + -
136A LYS* 3.6 1.0 - - - -
149A PHE* 3.6 5.5 - - - -
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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