Contacts of the helix formed by residues 89 - 100 (chain A) in PDB entry 2I91
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 GLN 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A SER* 4.0 13.4 + - - +
86A ALA* 4.2 11.5 + - - +
87A ALA 5.2 1.5 + - - +
88A LYS* 1.3 81.8 + - - +
90A GLU* 1.3 76.3 + - - +
91A PRO* 3.3 2.7 - - - -
92A THR* 2.9 29.1 + - - -
93A LEU* 2.9 28.4 + - + -
118A VAL 4.8 1.4 - - - +
120A ARG* 3.5 14.9 + - - -
124A HIS* 3.2 39.4 + - + +
11D U 5.5 0.2 + - - -
13D C 4.2 11.9 + - + +
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Residues in contact with GLU 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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42A GLU* 6.6 0.4 - - - -
88A LYS* 4.9 7.6 - - + +
89A GLN* 1.3 83.1 + - - +
91A PRO* 1.3 62.1 - - + +
93A LEU* 4.6 2.5 - - - +
94A PHE* 2.7 38.2 + - - +
127A THR* 4.2 16.9 + - + +
131A PHE* 3.4 23.9 - - + -
10D U 4.7 1.9 + - - -
11D U 3.9 18.0 + - - +
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Residues in contact with PRO 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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36A PHE* 3.3 44.8 - - + +
37A LEU* 3.9 16.2 - - - +
38A CYS 5.8 0.2 - - - -
39A PHE 5.0 0.2 - - - -
40A GLY* 3.5 27.8 - - - +
88A LYS* 4.1 15.5 - - + +
89A GLN 3.5 3.6 - - - -
90A GLU* 1.3 94.6 - - + +
92A THR* 1.3 55.5 + - - +
94A PHE* 4.5 0.9 - - + -
95A ALA* 3.0 29.6 + - - +
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Residues in contact with THR 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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37A LEU* 3.5 29.7 + - + +
77A ILE* 3.8 34.5 - - + +
80A PHE* 4.9 1.6 - - + -
81A SER* 4.4 15.7 - - - +
86A ALA* 5.0 4.5 - - + +
88A LYS 3.8 4.5 + - - -
89A GLN* 2.9 31.4 + - - -
91A PRO* 1.3 73.8 - - - +
93A LEU* 1.3 61.8 + - - +
95A ALA* 3.1 4.3 + - - +
96A LEU* 2.9 30.1 + - - +
118A VAL* 5.4 2.5 - - - -
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Residues in contact with LEU 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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89A GLN* 2.9 36.6 + - + +
90A GLU* 3.9 2.7 - - - +
92A THR* 1.3 77.2 - - - +
94A PHE* 1.3 60.9 + - - +
96A LEU* 3.5 3.8 + - + +
97A ALA* 3.1 23.0 + - - +
118A VAL* 3.9 29.2 - - + +
119A CYS* 4.0 12.6 - - - -
124A HIS* 3.2 41.5 - - + +
127A THR* 3.7 26.7 - - + -
128A PHE* 3.8 16.7 - - + -
131A PHE* 3.8 4.6 - - + -
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Residues in contact with PHE 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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36A PHE* 4.1 23.1 - + + -
54A GLY 5.7 1.3 - - - -
58A ALA* 5.0 20.2 - - + -
61A LEU* 5.5 2.9 - - + -
90A GLU 2.7 22.9 + - - +
91A PRO* 3.8 4.3 - - + +
93A LEU* 1.3 72.7 - - - +
95A ALA* 1.3 60.6 + - - +
97A ALA* 3.2 3.2 + - - +
98A VAL* 3.0 51.6 + - + +
131A PHE* 3.4 43.0 - + + -
134A ASP* 6.1 2.0 - - + -
135A LEU* 4.2 25.4 - - + -
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Residues in contact with ALA 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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33A LEU* 4.8 5.6 - - + -
36A PHE* 4.8 5.2 - - + -
37A LEU* 4.6 6.1 - - + -
61A LEU* 4.0 22.1 - - + +
77A ILE* 3.3 25.1 - - + -
91A PRO 3.0 18.6 + - - +
92A THR* 3.4 3.8 - - - +
94A PHE* 1.3 79.5 - - - +
96A LEU* 1.3 56.8 + - - +
98A VAL* 3.3 2.8 + - - +
99A CYS* 3.0 33.1 + - - -
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Residues in contact with LEU 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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74A VAL* 5.4 4.7 - - + -
77A ILE* 3.7 18.1 - - + +
78A LYS* 6.4 0.2 - - + -
92A THR 2.9 15.8 + - - +
93A LEU* 4.0 7.9 - - + +
95A ALA* 1.3 76.7 - - - +
97A ALA* 1.3 56.6 + - - +
99A CYS* 4.4 3.8 - - - -
100A SER* 3.1 21.7 + - - -
111A ALA* 3.5 34.7 - - + +
114A ALA* 4.7 9.2 - - + +
115A VAL* 3.8 7.6 - - + +
118A VAL* 3.8 39.5 - - + -
119A CYS* 5.9 1.1 - - - -
128A PHE* 3.2 28.3 - - + -
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Residues in contact with ALA 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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93A LEU 3.1 15.5 + - - +
94A PHE 3.3 8.7 - - - +
95A ALA 3.1 0.2 - - - -
96A LEU* 1.3 76.7 - - - +
98A VAL* 1.3 67.8 + - - +
100A SER* 2.9 21.6 + - - -
101A GLN* 3.2 9.7 - - - +
128A PHE* 3.6 17.5 - - + +
131A PHE* 3.7 25.6 - - + -
132A LYS* 4.4 5.4 - - + +
135A LEU* 3.9 11.0 - - + -
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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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58A ALA* 6.2 1.8 - - + -
61A LEU* 3.9 26.7 - - + -
62A LEU* 4.7 18.8 - - + -
65A ILE* 4.6 9.0 - - + -
94A PHE* 3.0 44.8 + - + +
95A ALA 3.3 5.1 + - - +
97A ALA* 1.3 74.2 - - - +
99A CYS* 1.3 64.4 + - - +
101A GLN* 2.9 15.7 + - + +
102A CYS* 2.9 13.7 + - + +
135A LEU* 3.8 19.1 - - + -
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Residues in contact with CYS 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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61A LEU* 4.5 4.9 - - - -
65A ILE* 4.4 11.7 - - - -
73A VAL* 3.7 29.8 - - - -
74A VAL* 4.1 15.5 - - + -
77A ILE* 4.5 1.1 - - - -
95A ALA 3.0 20.2 + - - +
96A LEU* 4.0 6.3 - - - +
98A VAL* 1.3 71.6 - - - +
100A SER* 1.3 58.2 + - - +
101A GLN 2.9 11.8 + - - -
102A CYS* 3.3 25.1 - - - -
107A THR* 3.8 21.3 - - + -
108A LYS* 3.5 11.6 + - - +
111A ALA* 4.0 4.5 - - + -
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Residues in contact with SER 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 LEU 3.1 16.7 + - - -
97A ALA* 2.9 14.1 + - - -
99A CYS* 1.3 74.6 - - - +
101A GLN* 1.3 57.4 + - - +
108A LYS* 3.4 17.0 - - - +
111A ALA* 3.8 12.5 - - - +
112A PHE* 3.4 25.0 - - - -
128A PHE* 4.0 10.3 - - - -
132A LYS* 2.6 41.6 + - - +
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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