Contacts of the strand formed by residues 20 - 24 (chain D) in PDB entry 5XVO
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 HIS 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D TYR* 3.4 12.3 - - - -
17D LYS* 2.8 31.7 + - + +
18D ASN* 2.9 28.5 + - + -
19D ASN* 1.3 80.4 - - - +
21D LEU* 1.3 67.3 + - - +
22D VAL* 4.7 0.2 - - + -
31D LEU* 4.2 27.5 - - + +
32D ILE* 3.3 11.5 + - - +
33D HIS* 3.4 37.8 + + + -
34D LEU* 4.4 1.1 - - - -
33F ILE* 3.0 30.2 + - + +
36F GLY* 4.0 10.5 - - - -
37F PHE 5.1 3.5 + - - -
38F ILE* 6.6 0.2 - - + -
97F ALA* 6.5 0.4 - - + -
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Residues in contact with LEU 21 (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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6D VAL* 4.4 22.2 - - + -
14D LEU* 4.3 21.3 - - + -
15D SER 3.8 2.0 - - - +
20D HIS* 1.3 73.9 - - - +
22D VAL* 1.3 66.1 + - - +
23D PHE* 5.1 2.2 - - + -
30D GLU 3.7 1.2 - - - +
31D LEU* 3.4 5.5 - - - -
32D ILE* 2.8 47.0 + - + +
34D LEU* 4.2 10.8 - - + +
37D ILE* 4.1 22.0 - - + -
40D LEU* 4.6 15.9 - - + -
53D LEU* 3.4 40.2 - - + -
57D LEU* 5.2 1.1 - - + -
106F LEU* 4.9 3.8 - - + -
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Residues in contact with VAL 22 (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 LYS 3.4 2.8 - - - +
14D LEU* 3.2 7.1 - - - +
15D SER* 2.8 51.0 + - - +
16D TYR 4.2 0.4 - - - -
17D LYS* 3.8 38.4 - - + +
20D HIS 4.0 2.2 - - - +
21D LEU* 1.3 77.6 - - - +
23D PHE* 1.3 60.9 + - - +
24D LYS* 4.0 29.2 - - + -
29D GLN* 4.4 3.6 - - - +
30D GLU 3.7 2.2 - - - +
31D LEU* 3.6 27.6 - - + -
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Residues in contact with PHE 23 (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 VAL* 4.0 5.6 - - + -
10D LYS* 4.4 6.7 - - + -
12D SER* 3.7 21.3 - - - -
13D LYS 3.9 2.0 - - - -
14D LEU* 3.9 19.1 - - + -
21D LEU* 4.0 4.4 + - + -
22D VAL* 1.3 72.4 - - - +
24D LYS* 1.3 59.7 + - - +
25D ALA* 3.6 33.2 - - + -
28D HIS* 4.0 20.0 - + - -
29D GLN* 3.4 6.4 - - - +
30D GLU* 2.9 53.0 + - + +
32D ILE* 6.1 0.9 - - + -
106F LEU* 3.3 56.1 - - + -
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Residues in contact with LYS 24 (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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12D SER* 3.3 3.0 - - - -
13D LYS* 2.8 53.2 + - + +
15D SER* 5.1 5.4 - - - +
22D VAL* 4.0 16.4 - - + -
23D PHE* 1.3 79.9 - - - +
25D ALA* 1.3 62.0 + - - +
28D HIS 4.1 2.9 - - - +
29D GLN* 3.8 33.8 + - + +
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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