Contacts of the strand formed by residues 101 - 105 (chain M) in PDB entry 1V7M
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 THR 101 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M GLN* 3.4 11.2 + - - +
7M SER 4.4 0.7 + - - -
8M PRO* 3.0 26.8 + - + +
9M GLY 3.6 2.5 - - - +
11M MET* 4.1 20.2 - - + -
21M ILE* 3.4 49.4 - - + +
83M ALA 3.3 3.1 - - - +
84M THR* 3.1 4.7 - - - -
85M TYR* 2.7 40.2 + - - +
100M GLY* 1.3 74.1 + - - -
102M LYS* 1.3 62.2 + - - +
103M LEU 3.5 0.7 + - - -
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Residues in contact with LYS 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M GLY 3.0 14.7 + - - +
10M ILE* 3.3 14.2 - - + +
11M MET* 2.8 33.8 + - - +
39M PRO* 6.3 2.9 - - - -
83M ALA 3.6 5.6 - - - +
84M THR* 3.5 24.4 - - + +
100M GLY 4.2 0.2 - - - -
101M THR* 1.3 71.8 - - - +
103M LEU* 1.3 57.9 + - - +
104M GLU* 2.6 41.0 + - + +
164M ASP* 5.5 9.3 - - - +
165M GLN* 6.1 4.2 - - - +
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Residues in contact with LEU 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M MET* 3.3 24.5 - - - +
13M ALA* 4.0 10.3 - - + +
19M VAL* 3.9 20.9 - - + -
21M ILE* 5.0 4.9 - - + -
74M ILE* 3.8 24.5 - - + -
77M MET* 3.9 26.0 - - + -
81M ASP 3.6 20.9 - - - +
82M ALA* 3.2 24.4 - - - +
83M ALA* 2.9 17.7 + - - +
85M TYR* 3.7 17.9 - - + -
101M THR 3.5 1.6 + - - +
102M LYS* 1.3 71.5 - - - +
104M GLU* 1.3 63.6 + - - +
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Residues in contact with GLU 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ILE* 4.3 17.9 - - + +
11M MET 2.7 17.1 + - - +
12M SER* 3.1 24.8 - - - -
13M ALA 3.3 4.7 + - - +
77M MET* 4.8 1.0 - - - +
82M ALA* 4.6 2.9 - - - -
102M LYS* 2.6 38.6 + - + +
103M LEU* 1.3 81.9 - - - +
105M ILE* 1.3 67.6 + - - +
165M GLN* 3.3 14.4 - - + +
172M TYR* 3.9 18.0 + - - +
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Residues in contact with ILE 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M SER* 4.3 4.6 - - - -
13M ALA 3.5 9.4 - - - +
14M SER* 5.8 0.2 - - - -
15M PRO* 4.7 17.5 - - + -
77M MET* 5.0 6.3 - - + -
79M ALA* 4.0 22.7 - - + +
82M ALA* 3.5 27.6 - - + -
104M GLU* 1.3 77.1 - - - +
106M LYS* 1.3 85.1 + - - +
107M ARG* 4.5 5.4 - - + -
139M TYR* 4.0 6.8 + - - -
165M GLN* 3.0 29.3 + - + +
166M ASP 6.1 0.4 - - - +
170M SER* 3.1 37.7 - - - +
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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