Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 2V40
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 GLY 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP 3.3 1.8 + - - -
41A GLU* 1.3 80.1 - - - +
43A LYS* 1.3 65.4 + - - +
44A GLY 3.2 2.5 - - - -
45A LYS* 3.2 19.1 + - - +
46A VAL* 3.6 5.4 + - - +
296A VAL* 3.8 9.3 - - - +
361A THR* 4.2 3.1 - - - +
1457A GDP 2.9 40.3 + - - -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.2 10.3 - - + +
34A LEU* 4.2 2.2 - - - -
35A GLY* 3.5 32.5 - - - +
39A GLY* 4.0 1.2 - - - -
40A ASP 3.9 8.1 - - - +
41A GLU* 2.8 27.0 + - - +
42A GLY* 1.3 75.7 - - - +
44A GLY* 1.3 58.6 - - - +
46A VAL* 3.0 5.6 + - - +
47A VAL* 2.9 33.7 + - + +
68A HIS* 5.6 3.6 - - - -
253A GLY 3.9 22.0 - - - +
254A ALA* 4.9 0.4 - - - +
255A ASN* 3.3 25.4 + - - +
296A VAL* 3.8 19.3 - - + +
1457A GDP 2.9 28.8 + - - +
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Residues in contact with GLY 44 (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 GLY 3.2 0.4 - - - -
43A LYS* 1.3 73.2 - - - +
45A LYS* 1.3 54.7 + - - +
47A VAL* 3.9 8.0 - - - +
48A ASP* 2.8 32.6 + - - +
68A HIS* 5.2 5.8 - - - -
84A SER* 5.9 5.5 - - - -
1457A GDP 2.8 27.5 + - - -
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Residues in contact with LYS 45 (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 GLY 3.3 12.6 - - - +
44A GLY* 1.3 78.7 - - - +
46A VAL* 1.3 60.9 + - + +
48A ASP* 3.5 8.1 - - - +
49A LEU* 3.5 22.7 + - + +
361A THR* 5.0 4.3 - - + -
444A GLY* 3.8 18.4 - - - -
446A GLY 2.9 20.0 + - - +
447A LYS 3.9 6.9 + - - +
448A SER 2.9 28.5 + - - -
449A ARG* 4.4 4.4 + - - +
451A SER 3.0 19.7 + - - -
452A MET* 3.8 21.7 - - + +
1457A GDP 3.1 38.7 + - + +
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Residues in contact with VAL 46 (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 VAL* 4.2 16.2 - - + -
42A GLY 3.6 11.4 + - - +
43A LYS 3.0 7.0 + - - +
45A LYS* 1.3 73.1 - - + +
47A VAL* 1.3 67.3 + - - +
49A LEU* 3.1 8.1 + - - +
50A LEU* 3.0 40.6 + - + +
294A TYR* 5.2 1.8 - - + -
296A VAL* 4.2 10.8 - - + -
359A ALA* 3.6 27.1 - - + -
361A THR* 5.0 2.2 - - + -
442A TRP* 4.0 23.8 - - + -
452A MET* 4.2 16.4 - - + -
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Residues in contact with VAL 47 (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 VAL* 4.0 27.1 - - + -
43A LYS* 2.9 24.4 + - + +
44A GLY* 3.9 7.0 - - - +
46A VAL* 1.3 76.1 - - - +
48A ASP* 1.3 54.0 + - - +
50A LEU* 4.5 5.6 - - - +
51A ALA* 2.7 42.4 + - + +
84A SER* 4.6 11.7 - - - -
85A GLY 4.6 0.4 - - - +
250A LEU* 4.3 7.9 - - + -
252A GLU* 3.3 49.4 - - + +
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Residues in contact with ASP 48 (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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44A GLY 2.8 22.9 + - - +
45A LYS* 3.5 9.5 - - - +
46A VAL 3.3 0.2 - - - -
47A VAL* 1.3 73.6 - - - +
49A LEU* 1.3 66.2 + - - +
51A ALA* 4.3 4.4 - - - +
52A GLN* 3.4 21.1 + - - +
70A VAL* 4.9 17.1 - - + +
449A ARG* 2.6 57.0 + - - +
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Residues in contact with LEU 49 (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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45A LYS* 3.5 10.3 + - + +
46A VAL* 3.1 7.9 + - - +
48A ASP* 1.3 81.1 - - - +
50A LEU* 1.3 66.7 + - + +
52A GLN* 3.5 27.7 + - - +
53A ASP* 4.6 2.4 + - - +
442A TRP* 3.9 20.0 - - + +
449A ARG* 3.9 35.2 - - + +
452A MET* 3.7 42.4 - - + -
454A GLN* 5.7 0.7 - - - +
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Residues in contact with LEU 50 (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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31A THR* 4.3 4.9 - - + -
33A VAL* 3.7 30.1 - - + -
46A VAL* 3.0 27.3 + - + +
47A VAL 4.0 2.0 - - - +
49A LEU* 1.3 76.0 - - + +
51A ALA* 1.3 65.0 + - - +
52A GLN 3.3 0.9 + - - -
53A ASP* 3.3 21.0 + - - +
54A ALA* 3.6 8.7 + - - +
250A LEU* 4.0 21.2 - - + +
294A TYR* 3.9 21.1 - - + +
441A LYS* 6.0 0.4 - - - -
442A TRP* 4.0 23.8 - - + -
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Residues in contact with ALA 51 (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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47A VAL* 2.7 23.9 + - + +
48A ASP* 4.3 4.7 - - - +
49A LEU 3.4 0.2 - - - -
50A LEU* 1.3 72.7 - - - +
52A GLN* 1.3 58.6 + - - +
53A ASP 3.2 0.9 + - - -
54A ALA* 3.3 13.8 + - - +
57A VAL* 4.3 3.4 - - + -
85A GLY* 3.7 31.2 - - - +
87A ILE* 6.1 1.8 - - + -
88A ASN* 2.8 24.2 + - + +
91A VAL* 3.9 1.4 - - - +
250A LEU* 3.9 15.0 - - + +
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Residues in contact with GLN 52 (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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48A ASP 3.4 16.8 + - - +
49A LEU* 3.5 24.1 - - - +
50A LEU 3.2 1.4 - - - -
51A ALA* 1.3 77.4 - - - +
53A ASP* 1.3 59.6 + - + +
88A ASN* 3.1 18.5 + - - +
449A ARG* 3.0 50.8 + - - +
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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