Contacts of the strand formed by residues 113 - 119 (chain K) in PDB entry 5A0Q
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 PRO 113 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8K GLN* 2.6 27.7 + - + +
9K GLY 3.8 18.8 - - - +
10K PRO 4.4 9.0 - - - +
12K TYR 3.6 7.0 - - - +
13K VAL* 3.2 25.4 - - + -
106K GLY 3.9 4.3 - - - +
107K TYR* 3.5 38.6 - - + +
111K GLU 4.9 0.9 - - - +
112K GLY* 1.3 86.5 - - - +
114K ALA* 1.3 55.9 + - - +
126K LYS* 4.7 2.4 + - - -
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Residues in contact with ALA 114 (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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8K GLN* 3.4 10.3 - - - +
13K VAL* 3.8 2.6 - - - +
77K PRO* 4.2 9.6 - - + +
104K LEU 4.1 1.4 - - - +
105K ALA 3.8 0.5 - - - -
106K GLY* 2.7 38.4 + - - +
111K GLU* 5.1 6.1 - - - +
112K GLY 3.6 6.2 + - - +
113K PRO* 1.3 75.5 - - - +
115K LEU* 1.3 61.3 + - - +
116K TYR* 3.5 29.6 - - + +
126K LYS* 4.3 10.1 - - - +
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Residues in contact with LEU 115 (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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6K GLY* 3.5 39.3 - - - +
7K ILE* 3.5 5.4 - - - +
8K GLN* 2.3 59.6 + - + +
13K VAL* 3.9 13.7 - - + -
103K LEU* 4.2 18.2 - - + -
104K LEU 3.7 4.5 - - - -
105K ALA* 4.3 8.5 - - + -
114K ALA* 1.3 73.9 - - - +
116K TYR* 1.3 68.9 + - - +
126K LYS* 3.9 4.0 - - - +
127K ALA* 3.0 42.4 + - + +
128K PRO 3.8 0.9 - - - +
129K PHE* 4.5 0.2 - - - -
130K ALA 4.3 7.0 - - - +
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Residues in contact with TYR 116 (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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77K PRO 4.3 3.4 - - - -
78K THR* 2.3 50.7 - - + +
81K ALA* 4.3 7.9 - - + -
82K ASN* 6.3 0.2 - - - -
102K LEU 3.8 0.7 - - - +
103K LEU* 3.3 10.6 - - - -
104K LEU 3.0 37.8 + - - +
111K GLU* 4.5 0.3 + - - -
114K ALA* 3.5 29.4 - - + +
115K LEU* 1.3 79.0 - - - +
117K TYR* 1.3 61.5 + - - +
118K MET* 4.1 8.5 - - + +
124K LEU* 3.5 37.0 - - + -
125K ALA 3.5 2.7 - - - +
126K LYS* 3.5 40.9 - - + +
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Residues in contact with TYR 117 (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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27J PHE* 4.7 6.5 - + - -
29J ILE* 3.6 35.2 - - + +
34J VAL* 4.0 35.4 - - + -
101K ASN* 4.1 12.4 + - - -
103K LEU* 3.9 2.5 - - - +
116K TYR* 1.3 74.3 - - - +
118K MET* 1.4 65.2 + - - +
119K ASP* 3.8 27.1 + - + -
123K ALA 4.1 8.3 - - - -
124K LEU* 3.6 0.5 - - - +
125K ALA* 3.1 36.2 + - + +
127K ALA* 4.1 8.3 - - + +
130K ALA* 4.3 16.4 - - + -
131K ALA 3.7 19.7 - - - -
132K HIS* 3.4 27.6 - + - -
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Residues in contact with MET 118 (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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81K ALA* 3.5 33.2 - - + +
84K THR* 3.6 23.8 - - + -
85K ARG* 5.3 4.5 - - + -
88K LEU* 5.1 9.2 - - + -
100K VAL 4.3 0.6 - - - +
101K ASN* 2.6 23.1 - - - +
102K LEU* 3.0 41.2 + - + +
104K LEU* 3.3 34.1 - - + +
116K TYR* 4.1 3.8 - - + -
117K TYR* 1.4 79.8 - - - +
119K ASP* 1.3 61.2 + - - +
122K ALA* 6.0 0.9 - - - -
123K ALA 4.2 3.8 - - - +
124K LEU* 3.6 20.2 - - + +
132K HIS* 3.8 0.2 - - - -
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Residues in contact with ASP 119 (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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27J PHE* 6.0 1.2 - - - -
29J ILE* 3.1 31.3 - - - +
88K LEU* 3.8 8.8 - - - +
100K VAL 4.1 0.4 - - - -
101K ASN* 3.6 6.7 - - - +
117K TYR* 3.8 17.0 + - + -
118K MET* 1.3 75.4 - - - +
120K TYR* 1.3 84.2 + - - +
121K LEU* 4.2 16.2 - - + +
122K ALA* 2.9 21.7 + - - +
123K ALA* 3.6 34.5 + - + +
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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