Contacts of the helix formed by residues 87 - 99 (chain A) in PDB entry 1JWG
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ASP* 3.5 18.8 - - - +
84A GLU* 2.8 49.2 + - - +
85A VAL 3.6 1.0 - - - +
86A GLY* 1.3 79.4 - - - +
88A PHE* 1.3 66.1 + - - +
89A ARG* 3.9 29.3 - - + +
90A PHE 3.0 4.7 + - - -
91A LEU* 2.9 23.5 + - - +
131A LYS* 4.3 5.6 - - + +
7C ASP* 3.5 24.2 - - + +
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Residues in contact with PHE 88 (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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87A LYS* 1.3 71.8 - - - +
89A ARG* 1.3 57.4 + - - +
91A LEU* 4.1 11.0 - - + -
92A ASN* 2.7 48.3 + - - +
131A LYS* 3.5 49.6 - - + -
134A GLU* 3.4 30.3 - - - -
135A ALA 4.6 0.4 - - - -
7C ASP* 2.7 17.6 + - + +
8C GLU 3.5 26.2 - - - +
9C ASP* 4.7 0.7 - - - -
10C LEU* 3.6 46.9 - - + +
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Residues in contact with ARG 89 (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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48A THR* 6.2 4.5 - - + -
84A GLU* 5.4 5.3 + - - +
87A LYS* 4.2 31.0 - - + +
88A PHE* 1.3 76.4 - - - +
90A PHE* 1.3 58.5 + - + +
92A ASN* 4.8 2.3 - - - +
93A GLU* 3.8 18.5 + - - +
7C ASP* 2.8 46.8 + - - +
8C GLU* 3.4 36.0 + - + +
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Residues in contact with PHE 90 (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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48A THR* 3.2 48.0 - - + +
51A LEU* 4.2 3.8 - - + -
52A ALA* 3.8 21.8 - - + -
55A ILE* 4.2 6.3 - - + -
70A LEU* 4.0 28.9 - - + -
84A GLU 3.7 19.3 - - - +
85A VAL* 3.7 32.1 - - + +
87A LYS* 3.0 4.9 + - - +
89A ARG* 1.3 78.3 - - - +
91A LEU* 1.3 67.8 + - - +
92A ASN 3.2 1.6 - - - -
93A GLU* 2.9 20.5 + - - +
94A LEU* 3.4 35.9 + - + +
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Residues in contact with LEU 91 (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 VAL 3.3 20.0 - - - +
86A GLY 3.9 7.6 - - - +
87A LYS 2.9 24.6 + - - +
88A PHE* 4.1 9.6 - - + -
90A PHE* 1.3 75.7 - - + +
92A ASN* 1.3 64.2 + - - +
94A LEU* 3.0 15.2 + - + +
95A ILE* 2.9 28.7 + - + +
119A LEU* 3.8 29.6 - - + -
122A TRP* 4.9 2.5 - - + -
131A LYS* 3.7 33.4 - - + +
132A ILE* 3.9 15.5 - - + -
135A ALA* 4.4 13.7 - - + -
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Residues in contact with ASN 92 (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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88A PHE* 2.7 31.9 + - - +
89A ARG* 4.8 3.4 - - - +
91A LEU* 1.3 72.7 - - - +
93A GLU* 1.3 65.6 + - - +
95A ILE* 3.3 7.5 + - - +
96A LYS* 3.1 30.0 + - - +
8C GLU* 4.1 9.5 - - - +
9C ASP 2.8 25.9 + - - -
10C LEU* 3.7 13.0 - - - +
11C LEU* 2.8 46.5 + - + +
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Residues in contact with GLU 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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52A ALA* 3.6 33.9 - - + +
55A ILE* 6.0 0.7 - - - -
56A GLN* 2.9 37.4 + - - +
89A ARG 3.8 18.9 - - - +
90A PHE* 2.9 10.7 + - + +
92A ASN* 1.3 79.3 - - - +
94A LEU* 1.3 61.1 + - + +
96A LYS* 3.1 32.9 + - - +
97A VAL* 3.4 13.3 - - - +
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Residues in contact with LEU 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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52A ALA* 6.0 0.2 - - - -
55A ILE* 3.9 39.3 - - + -
67A LEU* 4.5 5.2 - - + -
70A LEU* 4.3 4.5 - - + -
90A PHE* 3.4 32.5 + - + +
91A LEU* 3.0 13.9 + - + +
93A GLU* 1.3 76.1 - - + +
95A ILE* 1.3 66.7 + - + +
97A VAL* 3.2 20.5 + - - +
98A VAL* 3.4 10.2 + - - +
115A ILE* 4.0 21.3 - - + +
118A LEU* 6.4 0.4 - - + -
119A LEU* 3.9 30.1 - - + -
122A TRP* 4.0 13.9 - - + -
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Residues in contact with ILE 95 (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 LEU* 2.9 27.3 + - + +
92A ASN* 3.3 10.3 + - - +
94A LEU* 1.3 78.2 - - + +
96A LYS* 1.3 61.2 + - - +
98A VAL* 3.1 8.6 + - - +
99A SER* 2.7 42.9 + - - +
119A LEU* 5.5 2.7 - - + -
135A ALA* 4.1 14.1 - - + -
138A MET* 4.0 13.2 - - + -
139A LEU* 4.3 22.0 - - + -
10C LEU* 3.7 30.3 - - + -
11C LEU* 4.0 7.6 - - + -
13C ILE* 3.5 20.9 - - + -
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Residues in contact with LYS 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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56A GLN* 3.9 8.9 - - - +
92A ASN* 3.1 14.6 + - - +
93A GLU* 3.1 42.8 + - - +
95A ILE* 1.3 76.5 - - - +
97A VAL* 1.3 59.2 + - - +
98A VAL 3.5 0.3 + - - -
99A SER 3.7 1.6 - - - +
102A TYR* 3.3 32.9 - - + +
103A LEU* 2.8 39.5 + - + +
104A GLY 3.6 1.0 + - - -
11C LEU* 3.5 31.6 - - + +
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Residues in contact with VAL 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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55A ILE* 4.1 16.8 - - + +
56A GLN* 3.6 25.1 - - + -
93A GLU 3.4 16.8 - - - +
94A LEU* 3.2 9.2 + - - +
95A ILE 3.1 0.6 - - - -
96A LYS* 1.3 77.6 - - - +
98A VAL* 1.3 56.8 - - - +
103A LEU* 4.1 8.3 - - + -
104A GLY* 3.2 19.8 + - - -
107A THR* 3.4 31.1 + - + +
111A VAL* 3.8 7.9 - - + -
112A LYS* 3.7 6.4 - - + +
115A ILE* 3.4 25.8 - - + -
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Residues in contact with VAL 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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94A LEU 3.7 7.4 - - - +
95A ILE* 3.2 19.1 - - - +
97A VAL* 1.3 81.4 - - - +
99A SER* 1.3 63.0 + - - +
100A PRO* 3.6 7.4 - - - +
104A GLY* 4.1 3.4 - - - -
112A LYS* 3.7 47.1 + - + +
115A ILE* 4.0 21.3 - - + -
116A LEU* 4.2 12.6 - - + -
139A LEU* 4.3 19.1 - - + -
144A ILE* 3.9 22.4 - - + +
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Residues in contact with SER 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 ILE* 2.7 26.8 + - - +
96A LYS 3.7 0.4 + - - -
97A VAL 3.5 1.0 - - - -
98A VAL* 1.3 81.8 - - - +
100A PRO* 1.3 59.4 - - - +
101A LYS* 3.0 6.1 - - - -
102A TYR* 2.8 30.9 + - - -
103A LEU 3.4 1.4 + - - -
104A GLY 2.9 14.5 + - - -
144A ILE* 4.6 1.1 - - - +
13C ILE* 3.3 44.6 - - - +
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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