Contacts of the strand formed by residues 303 - 307 (chain B) in PDB entry 6B0Z
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 VAL 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 4.1 2.0 - - - +
68B ASN 2.9 9.5 + - - +
69B VAL* 3.6 2.2 - - + +
70B GLY 2.9 24.4 + - - +
294B VAL* 3.5 24.2 - - + -
295B LEU 3.4 7.6 - - - +
296B VAL* 4.3 19.7 - - + -
297B CYS* 5.6 0.2 - - - -
301B LYS 5.1 0.2 - - - -
302B THR* 1.3 82.9 - - - +
304B GLU* 1.3 66.2 + - - +
305B ALA* 4.5 4.9 - - + +
338B ARG 5.3 3.8 - - - +
339B GLY* 5.4 3.1 - - - -
342B HIS* 3.7 45.5 - - + +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B MET* 4.4 3.6 - - + +
64B ILE* 4.1 15.0 - - + -
70B GLY 3.4 10.5 - - - +
72B LYS* 3.4 31.3 - - - +
96B ASN* 6.0 0.5 - - - -
99B ILE* 3.8 23.9 - - - +
100B ARG* 5.8 1.0 - - - +
103B LEU* 4.4 14.6 - - + -
294B VAL* 3.4 1.6 - - - -
295B LEU* 2.7 62.0 + - + +
297B CYS* 5.6 0.4 - - - -
303B VAL* 1.3 74.4 - - - +
305B ALA* 1.3 64.8 + - - +
306B GLU* 4.0 19.5 - - - +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLY 2.9 10.7 + - - +
71B VAL* 3.4 3.3 - - - -
72B LYS* 3.0 26.0 + - - +
293B SER 3.7 8.1 - - - +
294B VAL* 4.3 7.4 - - + +
303B VAL* 4.2 2.4 - - + -
304B GLU* 1.3 74.8 - - - +
306B GLU* 1.3 62.8 + - - +
335B ALA* 3.4 29.1 - - - +
338B ARG* 4.1 17.5 - - + -
339B GLY* 4.2 6.1 - - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS* 3.7 26.3 + - + +
73B CYS 6.0 0.4 - - - -
74B ALA* 6.0 0.2 - - - -
96B ASN* 3.4 24.0 - - - +
292B THR* 4.3 3.1 + - - -
293B SER* 2.8 50.0 + - - +
294B VAL* 5.7 0.2 - - - -
295B LEU* 5.7 2.9 + - - +
304B GLU* 4.0 21.0 - - - +
305B ALA* 1.3 77.5 - - - +
307B ALA* 1.3 70.9 + - - +
308B ALA* 5.5 0.2 - - - -
331B ALA 4.7 0.4 - - - -
335B ALA* 3.6 14.5 - - - +
501B NDP 3.7 11.8 + - - -
503B FLC 5.6 1.7 - - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TRP* 6.5 0.2 - - + -
72B LYS 4.5 3.2 + - - -
74B ALA* 6.0 2.1 - - + +
291B MET 4.1 4.0 - - - -
292B THR* 5.0 0.4 - - - +
306B GLU* 1.3 91.1 - - - +
308B ALA* 1.3 63.7 + - - +
309B HIS* 3.3 42.4 + - + +
331B ALA* 3.7 24.0 - - + -
332B SER* 3.9 6.0 - - - +
335B ALA* 4.0 5.5 - - - +
501B NDP 4.5 4.0 + - - -
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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