Contacts of the helix formed by residues 41 - 47 (chain D) in PDB entry 2V5P
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 41 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE 3.8 13.5 - - - -
29D SER* 5.1 1.6 - - - -
40D ARG* 1.3 77.6 - - - +
42D ILE* 1.3 64.2 + - - -
43D VAL* 3.3 4.0 - - - -
44D GLU* 3.1 17.3 + - - +
45D GLU* 3.3 21.0 + - - +
59D TYR* 3.5 10.1 + - - -
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 4.8 8.9 - - + +
17D LEU* 3.8 23.1 - - + -
27D TYR 4.5 0.4 - - - +
28D PHE* 3.6 46.4 + - + +
41D GLY* 1.3 70.7 - - - -
43D VAL* 1.3 66.6 + - + +
45D GLU* 4.4 2.2 - - - +
46D CYS* 2.9 42.7 + - + +
56D LEU* 3.8 20.0 - - + +
59D TYR* 3.6 51.6 + - + -
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.5 13.0 - - + -
28D PHE* 4.7 13.0 - - + +
41D GLY* 3.3 1.1 - - - -
42D ILE* 1.3 88.3 - - + +
44D GLU* 1.3 58.2 + - + +
47D CYS* 3.0 33.6 + - + +
48D PHE* 2.8 38.9 + - + -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.3 27.9 + - - +
41D GLY* 3.1 30.3 + - - +
42D ILE 3.2 0.4 - - - -
43D VAL* 1.3 82.2 - - + +
45D GLU* 1.3 58.6 + - - +
48D PHE* 3.2 33.3 - - + +
49D ARG* 2.8 37.1 + - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 5.4 8.4 - - + +
41D GLY 3.3 10.8 + - - +
42D ILE* 3.2 7.7 + - - +
44D GLU* 1.3 81.8 - - - +
46D CYS* 1.3 62.8 + - - +
49D ARG* 3.7 15.3 - - - +
50D SER 3.7 11.4 - - - +
51D CYS* 3.6 17.6 - - + +
55D LEU* 3.4 42.9 - - + +
58D THR* 5.2 1.2 - - - +
59D TYR* 4.0 20.5 + - + -
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Residues in contact with CYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.1 31.2 + - + +
13D LEU* 3.8 14.6 - - + -
42D ILE* 2.9 20.0 + - - +
45D GLU* 1.3 79.3 - - - +
47D CYS* 1.3 58.8 + - - +
49D ARG 3.0 18.5 - - - +
51D CYS* 2.0 50.7 - - - +
55D LEU 4.4 7.4 - - - -
56D LEU* 3.8 15.3 - - - -
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Residues in contact with CYS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D THR* 3.3 16.5 - - - +
8D LEU 3.5 10.5 - - - +
9D CYS* 2.0 62.7 - - - -
10D GLY 4.8 1.1 - - - -
13D LEU* 4.8 2.9 - - + -
42D ILE 4.1 0.2 + - - -
43D VAL* 3.0 35.3 + - + +
46D CYS* 1.3 78.9 - - - +
48D PHE* 1.3 68.5 + - - +
49D ARG 3.2 1.1 - - - -
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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