Contacts of the strand formed by residues 60 - 68 (chain M) in PDB entry 1VQM
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 VAL 60 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360 C 5.1 1.2 + - - -
39M ARG* 4.8 5.0 + - - -
54M TYR* 3.5 27.4 - - + -
55M LYS* 3.4 32.1 - - + +
57M LYS* 3.3 25.4 + - + +
59M GLY* 1.3 80.8 + - - +
61M ILE* 1.3 66.1 + - - +
62M VAL* 5.4 0.2 - - - +
132M ILE* 4.3 6.7 - - + -
133M LEU 3.7 3.1 - - - -
134M ILE* 4.0 21.3 - - + -
141M ILE* 4.4 6.7 - - + -
147M LEU* 4.5 13.7 - - + -
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Residues in contact with ILE 61 (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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1350 G 3.7 22.4 - - - +
1360 C 4.6 1.1 - - - +
39M ARG* 3.7 47.1 - - + +
59M GLY* 3.5 21.3 - - - +
60M VAL* 1.3 82.2 - - - +
62M VAL* 1.3 74.9 + - - +
109M PHE* 4.4 11.9 - - + -
112M LEU* 3.9 33.2 - - + -
132M ILE* 3.4 5.2 - - - +
133M LEU* 2.7 43.7 + - + +
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Residues in contact with VAL 62 (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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39M ARG* 3.6 5.7 - - - +
40M ILE* 2.8 59.0 + - + +
41M GLU 5.6 1.3 - - - +
42M ARG* 5.5 0.4 - - - -
43M PRO* 3.9 20.9 - - + -
54M TYR* 3.7 35.0 - - + -
60M VAL 5.4 0.2 - - - +
61M ILE* 1.3 83.2 - - - +
63M ALA* 1.3 63.8 + - - +
118M TYR* 4.5 2.7 - - - +
130M GLU* 4.3 15.0 - - + -
131M VAL 3.3 10.3 - - - +
132M ILE* 4.7 8.1 - - + -
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Residues in contact with ALA 63 (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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37M VAL* 4.1 10.1 - - + -
38M GLU 3.3 10.8 - - - +
39M ARG* 4.0 1.6 - - - -
40M ILE* 4.3 1.1 - - - +
62M VAL* 1.3 77.3 - - - +
64M ARG* 1.3 61.4 + - - +
65M VAL* 3.9 1.4 + - - +
105M ALA* 5.1 3.4 - - + -
109M PHE* 3.7 35.4 - - + -
129M HIS 3.8 0.5 - - - +
130M GLU* 3.4 3.0 - - - -
131M VAL* 2.8 38.7 + - - +
133M LEU* 4.4 7.8 - - + +
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Residues in contact with ARG 64 (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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55F GLN* 5.5 5.9 - - - +
31M TRP* 2.8 65.5 - - - +
34M GLU* 3.1 19.9 + - - -
36M ALA 3.7 0.7 - - - +
37M VAL* 3.4 2.9 - - - -
38M GLU* 2.8 40.7 + - + +
40M ILE* 4.2 24.4 - - + +
44M THR* 3.7 6.5 + - - -
63M ALA* 1.3 73.2 - - - +
65M VAL* 1.3 62.2 + - - +
128M TRP* 3.8 23.8 - - + -
129M HIS 3.4 9.9 - - - +
130M GLU* 3.4 31.5 + - + +
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Residues in contact with VAL 65 (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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36M ALA* 3.1 11.4 - - + +
37M VAL* 4.0 18.6 - - + -
63M ALA 4.2 6.1 - - - +
64M ARG* 1.3 80.5 - - - +
66M SER* 1.3 72.8 + - - +
67M VAL* 4.4 2.2 - - + -
101M ALA* 3.8 32.9 - - + +
104M ARG* 4.4 8.7 - - + -
105M ALA* 3.7 30.1 - - + -
127M LYS 3.6 0.9 - - - +
128M TRP* 3.3 5.8 - - - -
129M HIS* 2.8 38.8 + - - +
131M VAL* 4.5 3.1 - - + -
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Residues in contact with SER 66 (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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14680 G 4.7 7.0 + - - -
31M TRP 5.7 0.3 + - - -
35M GLY 3.8 16.5 + - - -
36M ALA* 3.1 15.8 + - - +
65M VAL* 1.3 76.6 - - - +
67M VAL* 1.3 70.5 + - - +
104M ARG* 4.0 7.1 + - - -
126M GLN* 4.0 16.1 + - - -
127M LYS 3.2 6.7 - - - -
128M TRP* 3.2 29.8 - - - -
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Residues in contact with VAL 67 (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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14680 G 5.5 1.3 - - - -
65M VAL* 4.4 2.7 - - + -
66M SER* 1.3 81.6 - - - +
68M ARG* 1.3 87.6 + - - +
97M ILE* 3.7 27.8 - - + +
100M VAL* 4.5 8.7 - - + -
101M ALA* 4.1 33.0 - - + +
104M ARG* 3.8 24.2 - - - +
126M GLN* 3.1 6.0 - - - -
127M LYS* 2.9 33.3 + - - +
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Residues in contact with ARG 68 (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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14680 G 4.9 7.5 + - - +
14690 C 2.9 41.3 + - - +
14700 A 2.6 37.5 + - - -
67M VAL* 1.3 89.2 - - - +
69M LYS* 1.3 71.5 + - - +
70M GLY 3.5 7.9 + - - -
71M SER 2.9 29.3 + - - -
72M ALA* 4.1 1.2 - - - +
73M ARG* 3.1 22.3 - - - +
93M ARG* 5.1 2.6 - - - +
97M ILE* 4.0 11.9 - - - +
104M ARG* 5.0 0.8 - - - +
125M ARG 3.8 8.1 - - - +
126M GLN* 4.4 1.8 - - - +
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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