Contacts of the strand formed by residues 53 - 57 (chain K) in PDB entry 5GAG
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 TYR 53 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A G 4.9 1.8 - - - -
8A C 3.4 45.4 - - - -
13K ARG* 3.4 44.7 + - + +
14K ASP 3.3 15.0 + - - -
15K TRP* 3.5 53.6 - + + -
16K TYR* 3.1 24.4 + - - +
52K ASP* 1.3 73.6 - - - +
54K ILE* 1.3 59.5 + - - +
121K LYS* 3.3 37.8 - - + +
123K LYS* 4.9 1.1 - - - -
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Residues in contact with ILE 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K TYR* 3.7 15.5 - - + +
18K VAL* 4.0 21.8 - - + -
32K LEU* 3.7 37.7 - - + +
35K ARG* 4.2 17.0 - - + -
36K LEU* 4.0 10.8 - - + -
52K ASP* 3.4 17.5 - - + +
53K TYR* 1.3 74.2 - - - +
55K ILE* 1.3 75.2 + - - +
56K VAL* 4.6 4.7 - - + -
121K LYS 3.0 7.8 + - - +
122K LEU* 3.7 16.4 - - + +
123K LYS* 2.9 28.4 + - - +
140K LEU* 5.0 2.7 - - + -
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Residues in contact with ILE 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K TRP* 4.3 10.8 - - + -
16K TYR 3.0 10.1 + - - +
17K VAL* 3.4 10.7 - - + -
18K VAL 2.8 25.6 + - - -
54K ILE* 1.3 77.3 - - - +
56K VAL* 1.3 68.5 + - - +
57K LEU* 3.6 29.2 - - + -
123K LYS* 3.1 11.4 - - + +
125K TYR* 3.9 11.9 - - + -
130K HIS* 4.0 12.3 - - + -
132K HIS* 3.8 38.6 - - + -
137K PRO* 3.9 25.1 - - + -
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Residues in contact with VAL 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K VAL* 3.4 9.2 - - + +
20K ALA* 4.0 18.2 - - + -
28K LEU* 5.0 1.1 - - + -
32K LEU* 3.8 33.0 - - + -
54K ILE* 4.6 2.5 - - + -
55K ILE* 1.3 80.4 - - - +
57K LEU* 1.3 63.8 + - - +
101K ILE* 3.9 30.7 - - + -
122K LEU* 4.1 16.8 - - + -
123K LYS 2.8 9.7 + - - -
124K VAL* 3.4 11.9 - - + +
125K TYR 3.0 30.0 + - - +
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Residues in contact with LEU 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K VAL* 3.9 20.9 - - + -
18K VAL 2.9 11.2 + - - +
19K ASP* 3.0 25.0 - - + +
20K ALA* 3.1 15.6 + - - +
55K ILE* 3.6 19.5 - - + -
56K VAL* 1.3 76.3 - - - +
58K ASN* 1.3 69.9 + - - +
59K ALA 3.4 0.4 + - - -
125K TYR* 4.1 14.4 - - + -
127K GLY 4.4 7.4 - - - +
128K ASN* 3.3 33.7 - - - +
129K GLU 4.6 0.7 - - - -
130K HIS* 3.9 23.8 - - + -
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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