Contacts of the strand formed by residues 106 - 110 (chain P) in PDB entry 2IMW
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 GLU 106 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5P PHE* 3.7 20.1 - - + -
6P VAL 3.3 3.8 - - - -
7P ASP* 3.3 16.3 - - - +
89P MET* 3.9 3.7 - - - +
101P ILE* 3.7 1.2 - - - -
102P ALA* 2.9 35.3 + - + +
103P SER* 3.3 16.8 + - - +
104P ILE 3.7 0.2 - - - -
105P ASP* 1.3 95.7 - - - +
107P ALA* 1.3 62.0 + - - +
108P TYR* 4.9 1.4 + - - -
152P LYS* 3.1 29.4 + - - -
159P LYS* 5.0 0.5 + - - -
401P DDS 4.7 5.2 + - - -
1918T C 3.2 38.4 + - - +
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Residues in contact with ALA 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P LEU 3.9 1.2 - - - +
5P PHE* 3.5 3.9 - - - -
6P VAL* 2.9 33.9 + - - +
8P PHE* 5.7 0.6 - - + -
89P MET* 3.8 24.2 - - - -
92P LEU* 3.9 16.8 - - + -
99P ILE* 4.4 10.1 - - + -
100P GLU 3.2 12.3 - - - +
101P ILE* 4.2 3.8 - - - -
102P ALA 4.4 0.2 - - - +
106P GLU* 1.3 75.6 - - - +
108P TYR* 1.3 63.7 + - - +
109P LEU* 4.0 3.7 - - + +
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Residues in contact with TYR 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P VAL* 4.0 8.5 - - + -
4P LEU 3.8 2.2 - - - -
5P PHE* 3.3 40.6 - + + -
98P LYS 3.9 0.3 - - - +
99P ILE* 3.3 6.2 - - - +
100P GLU* 2.7 52.5 + - + +
102P ALA* 3.8 20.4 - - + -
106P GLU* 4.9 1.4 + - - -
107P ALA* 1.3 74.4 - - - +
109P LEU* 1.3 61.6 + - - +
110P ASP 4.2 0.4 - - - -
148P LYS* 3.4 50.8 + - + -
152P LYS* 3.5 28.8 + - + +
237P ILE* 4.0 18.9 - - + +
240P ARG* 4.3 9.2 - - - -
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Residues in contact with LEU 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P VAL* 3.5 3.1 - - - +
4P LEU* 2.8 46.9 + - + +
6P VAL* 4.6 4.7 - - + -
92P LEU* 3.6 44.0 - - + +
95P TYR* 4.0 17.9 - - + -
96P SER* 4.1 13.5 - - - -
98P LYS 3.5 3.6 - - - +
99P ILE* 4.2 16.6 - - + -
107P ALA 4.0 10.5 - - - +
108P TYR* 1.3 80.5 - - - +
110P ASP* 1.3 61.2 + - - +
111P ILE* 3.4 14.5 + - + -
128P ILE* 4.4 14.6 - - + -
237P ILE* 4.5 3.4 - - - -
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Residues in contact with ASP 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P MET* 3.8 24.1 - - - +
2P ILE 3.8 3.4 - - - -
96P SER* 2.7 23.9 + - - -
98P LYS* 2.9 47.7 + - + +
109P LEU* 1.3 69.5 - - - +
111P ILE* 1.3 56.2 + - - +
112P SER* 2.7 32.5 + - - -
113P ASP* 4.7 1.9 + - - +
114P LYS* 5.1 0.9 - - - +
237P ILE* 4.1 23.6 + - + +
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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