Contacts of the helix formed by residues 86 - 98 (chain A) in PDB entry 2IMT
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TYR* 4.3 1.6 + - - +
42A ARG* 3.8 23.4 - - - +
82A GLY* 3.0 27.1 + - - +
85A ILE* 1.3 81.5 - - + +
87A ARG* 1.3 65.7 + - - +
88A ARG 3.1 3.0 + - - -
89A TYR* 3.2 15.0 + - - +
90A ASP* 2.9 35.5 + - - +
93A PHE* 4.7 2.4 - - - -
126A GLY 4.9 0.7 - - - +
129A VAL* 4.3 7.3 - - + +
130A ALA* 3.2 34.4 + - - +
133A GLY* 4.1 10.1 - - - -
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Residues in contact with ARG 87 (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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82A GLY 4.2 2.2 + - - -
83A ASP* 3.1 39.6 + - - +
84A ASP* 3.9 24.5 + - - +
85A ILE 3.2 2.4 - - - -
86A ASN* 1.3 77.9 - - - +
88A ARG* 1.3 59.1 + - + +
90A ASP* 3.5 5.7 + - - +
91A SER* 3.1 29.3 + - - -
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Residues in contact with ARG 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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85A ILE 4.7 12.2 + - - -
86A ASN 3.3 0.6 - - - -
87A ARG* 1.3 77.8 - - + +
89A TYR* 1.3 126.0 + - - +
90A ASP 3.4 0.2 + - - -
91A SER* 3.5 11.7 + - - +
92A GLU* 3.5 21.9 + - - +
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Residues in contact with TYR 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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85A ILE* 5.0 1.8 - - + -
86A ASN* 3.2 19.6 + - - +
88A ARG* 1.3 122.8 + - - +
90A ASP* 1.3 57.4 + - - +
92A GLU* 3.3 11.2 + - - +
93A PHE* 3.0 51.8 + + + -
118A LEU* 3.7 24.2 - - + +
126A GLY 4.3 9.8 - - - -
127A ARG* 3.8 23.7 + - - +
130A ALA* 3.4 25.6 - - + -
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Residues in contact with ASP 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 ARG* 2.7 30.0 + - - -
86A ASN* 2.9 23.9 + - - +
87A ARG* 3.5 7.4 - - - +
89A TYR* 1.3 76.2 - - - +
91A SER* 1.3 62.0 + - - +
93A PHE* 3.1 9.6 + - - +
94A GLN* 2.9 35.7 + - - +
137A ARG* 2.8 39.7 + - - +
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Residues in contact with SER 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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87A ARG 3.1 14.4 + - - -
88A ARG* 4.1 6.3 - - - -
89A TYR 3.4 0.4 - - - -
90A ASP* 1.3 81.5 - - - +
92A GLU* 1.3 62.3 + - - +
94A GLN* 3.6 13.0 + - - +
95A THR* 3.3 24.1 + - - -
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Residues in contact with GLU 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 ARG* 3.5 16.3 + - - +
89A TYR* 3.3 11.9 + - - +
90A ASP 3.0 0.6 - - - -
91A SER* 1.3 79.8 - - - +
93A PHE* 1.4 53.1 - - - +
94A GLN 3.0 1.8 - - - -
95A THR* 3.0 8.1 + - - +
96A MET* 2.7 56.3 + - - +
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Residues in contact with PHE 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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86A ASN* 4.7 2.7 - - - -
89A TYR* 3.0 54.0 + + + -
90A ASP* 3.1 12.3 + - - +
92A GLU* 1.4 74.1 - - + +
94A GLN* 1.3 59.0 + - - +
96A MET* 3.4 18.2 - - + -
97A LEU* 2.8 42.3 + - + +
114A ILE* 3.9 16.4 - - + -
118A LEU* 4.2 13.5 - - + -
130A ALA* 3.3 28.9 - - - -
133A GLY 4.2 5.4 - - - -
134A PHE* 3.5 41.7 - + + -
137A ARG* 4.1 15.5 - - + -
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Residues in contact with GLN 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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90A ASP* 2.9 20.0 + - - +
91A SER* 3.7 11.4 - - - +
92A GLU 3.0 0.2 - - - -
93A PHE* 1.3 79.1 - - - +
95A THR* 1.3 61.1 + - - +
97A LEU* 4.6 4.3 - - - +
98A GLN* 3.3 26.9 + - - +
137A ARG* 3.7 46.7 + - - +
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Residues in contact with THR 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 SER* 3.3 13.4 + - - -
92A GLU* 3.0 10.4 + - - -
94A GLN* 1.3 79.7 - - - +
96A MET* 1.3 63.1 + - - +
98A GLN* 3.2 32.6 + - - +
99A HIS* 4.5 1.4 + - - +
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Residues in contact with MET 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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92A GLU* 2.7 49.8 + - - +
93A PHE* 3.4 24.7 - - + +
95A THR* 1.3 74.6 - - - +
97A LEU* 1.3 48.6 + - + +
99A HIS* 2.2 44.2 + - + -
110A TYR* 3.3 19.1 - - + +
114A ILE* 3.5 40.8 - - + -
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Residues in contact with LEU 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 PHE* 2.8 24.5 + - + +
94A GLN* 4.6 3.6 - - - +
96A MET* 1.3 73.2 - - - +
98A GLN* 1.4 54.3 + - - +
99A HIS* 3.0 7.6 - - - -
100A LEU* 2.7 48.2 + - + +
110A TYR* 3.6 31.0 - - + -
134A PHE* 4.0 15.9 - - + -
137A ARG* 3.5 42.8 - - + +
138A LEU* 3.7 12.3 - - + +
141A HIS* 3.1 22.2 - - + +
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Residues in contact with GLN 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 GLN* 3.3 23.2 + - - +
95A THR* 3.2 24.2 + - - +
97A LEU* 1.4 76.5 - - - +
99A HIS* 1.3 58.7 + - - +
100A LEU 4.7 0.3 - - - +
141A HIS* 3.6 18.6 - - - +
145A HIS* 4.3 9.5 - - - -
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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