Contacts of the strand formed by residues 20 - 24 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L TYR* 3.5 12.7 - - - -
17L LYS 2.8 32.1 + - - +
18L ASN* 2.9 27.8 + - + -
19L ASN* 1.3 80.1 - - - +
21L LEU* 1.3 68.0 + - - +
22L VAL* 3.7 0.4 + - + -
31L LEU* 4.2 26.3 - - + +
32L ILE 3.3 11.3 + - - +
33L HIS* 3.4 25.7 + + + -
34L LEU* 4.4 1.8 - - - -
33N ILE* 3.2 25.7 + - + +
36N GLY* 3.8 24.7 - - - -
37N PHE 5.3 2.2 + - - -
38N ILE* 6.5 0.7 - - + -
97N ALA* 6.2 3.6 - - + -
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Residues in contact with LEU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L VAL* 4.5 10.5 - - + -
14L LEU* 4.4 14.1 - - + -
15L SER 3.8 1.3 - - - -
20L HIS* 1.3 73.5 - - - +
22L VAL* 1.3 66.3 + - - +
23L PHE* 4.0 1.5 + - + +
30L GLU 3.7 1.2 - - - +
31L LEU* 3.4 4.7 - - - -
32L ILE* 2.8 46.4 + - + +
34L LEU* 4.2 7.8 - - + +
37L ILE* 4.0 26.0 - - + -
40L LEU* 4.3 26.5 - - + -
53L LEU* 3.2 44.4 - - + -
57L LEU* 5.4 0.9 - - + -
106N LEU* 5.1 6.7 - - + -
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Residues in contact with VAL 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LYS 3.4 2.3 - - - +
14L LEU* 3.3 7.4 - - - +
15L SER* 2.8 51.9 + - - +
16L TYR 4.2 0.2 - - - -
17L LYS* 3.7 41.3 - - + +
20L HIS 4.0 1.8 - - - +
21L LEU* 1.3 76.9 - - - +
23L PHE* 1.3 62.3 + - - +
24L LYS* 4.1 25.8 - - + -
29L GLN* 4.8 4.3 - - + +
30L GLU 3.7 3.4 - - - +
31L LEU* 3.6 28.5 - - + -
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Residues in contact with PHE 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L VAL* 4.1 3.4 - - + -
10L LYS* 4.6 7.0 - - + -
12L SER* 3.3 25.6 - - - -
13L LYS 3.9 1.6 - - - -
14L LEU* 3.6 19.5 - - + -
21L LEU* 4.0 3.7 + - + -
22L VAL* 1.3 73.1 - - - +
24L LYS* 1.3 58.6 + - - +
25L ALA* 3.6 30.3 - - + -
28L HIS* 4.8 14.6 - + - -
29L GLN* 3.3 7.8 - - - +
30L GLU* 2.9 52.3 + - + +
32L ILE* 6.1 0.9 - - + -
106N LEU* 3.4 64.6 - - + -
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Residues in contact with LYS 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L SER* 3.3 5.4 - - - -
13L LYS* 2.8 53.5 + - + +
15L SER* 4.7 8.3 - - - +
17L LYS* 6.3 1.3 - - - +
22L VAL* 4.0 20.6 + - + -
23L PHE* 1.3 76.4 - - - +
25L ALA* 1.3 61.9 + - - +
28L HIS 4.1 1.3 - - - -
29L GLN* 3.8 28.9 - - + +
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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