Contacts of the strand formed by residues 4 - 9 (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 LEU 4 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K TYR* 1.3 87.6 - - - +
5K ILE* 1.3 62.5 + - - +
16K ALA 3.7 5.4 - - - +
17K SER* 3.5 26.7 - - - +
34K LYS* 4.1 19.5 - - + -
45K LEU* 3.1 41.7 - - + +
47K VAL* 3.6 32.5 - - + +
101K ASN 3.9 3.6 - - - +
103K LEU* 4.7 1.6 - - + +
131K ALA* 3.1 9.1 - - - +
132K HIS* 3.0 46.4 + - + +
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Residues in contact with ILE 5 (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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3K TYR* 3.6 32.3 - - + +
4K LEU* 1.3 75.2 - - - +
6K GLY* 1.3 58.1 + - - +
7K ILE* 4.8 3.6 - - + -
15K VAL* 3.4 5.2 - - - +
16K ALA* 3.0 45.5 + - + +
45K LEU* 4.4 0.7 - - - +
103K LEU* 4.0 7.2 - - - +
130K ALA 3.3 20.4 - - - +
131K ALA* 4.0 6.3 - - + -
139K THR* 5.3 1.6 - - - -
140K LEU* 5.5 0.7 - - + -
143K LEU* 3.3 31.2 - - + -
160K LEU* 3.6 33.0 - - + -
163K CYS* 5.1 8.1 - - + -
164K LEU* 5.8 2.9 - - + -
178K PHE* 6.0 2.2 - - + -
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Residues in contact with GLY 6 (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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5K ILE* 1.3 75.0 - - - +
7K ILE* 1.3 67.7 + - - +
14K LEU 3.4 9.6 - - - -
103K LEU* 3.8 9.2 - - - +
115K LEU* 3.5 20.9 - - - -
129K PHE* 3.4 3.1 - - - +
130K ALA 2.9 29.5 + - - +
143K LEU* 3.7 2.1 - - - +
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Residues in contact with ILE 7 (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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5K ILE* 4.8 2.5 - - + -
6K GLY* 1.3 79.9 - - - +
8K GLN* 1.3 65.6 + - - +
9K GLY 4.0 0.2 - - - -
12K TYR* 4.2 14.4 - - + +
13K VAL* 3.5 8.0 - - - +
14K LEU* 3.0 54.5 + - + +
115K LEU* 3.5 3.5 - - - +
128K PRO 3.9 4.9 - - - -
129K PHE* 4.2 2.5 - - + +
143K LEU* 3.8 21.5 - - + -
147K TYR* 3.3 33.0 - - + +
156K ALA* 4.6 2.9 - - + +
159K LEU* 3.9 23.6 - - + -
160K LEU* 4.6 15.0 - - + +
163K CYS* 6.2 0.9 - - - -
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Residues in contact with GLN 8 (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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7K ILE* 1.3 73.4 - - - +
9K GLY* 1.3 60.1 - - - +
12K TYR 4.4 3.6 - - - +
13K VAL* 4.8 1.6 - - + +
113K PRO* 2.6 34.6 + - + +
114K ALA* 3.5 5.4 - - - +
115K LEU* 2.3 44.4 + - + +
126K LYS* 3.6 21.0 - - - +
127K ALA 3.6 4.0 - - - +
128K PRO* 2.9 27.0 + - + +
147K TYR* 2.1 33.6 + - - -
149K PRO 5.3 0.7 - - - +
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Residues in contact with GLY 9 (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* 1.3 76.8 - - - +
10K PRO* 1.3 77.7 - - - +
11K ASP 2.9 5.0 + - - -
12K TYR* 2.9 42.9 + - - +
113K PRO* 3.8 8.5 - - - +
147K TYR* 3.5 4.9 - - - -
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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