Contacts of the strand formed by residues 303 - 307 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.9 6.3 - - - +
68A ASN 3.1 8.6 + - - +
69A VAL* 3.6 1.8 - - - -
70A GLY 3.0 23.5 + - - +
103A LEU* 5.8 0.2 - - - -
294A VAL* 3.6 24.2 - - + -
295A LEU 3.5 9.0 - - - +
296A VAL* 4.8 13.0 - - + -
297A CYS* 5.9 0.2 - - - -
300A GLY 5.9 0.9 - - - +
302A THR* 1.3 80.3 - - - +
304A GLU* 1.3 66.3 + - - +
305A ALA* 4.3 7.0 - - + +
338A ARG* 5.2 4.5 - - + +
339A GLY* 5.2 3.4 - - - -
342A HIS* 3.7 44.9 - - + +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 4.5 2.4 - - + +
64A ILE* 3.7 23.1 - - + -
70A GLY 3.4 9.0 - - - +
72A LYS* 3.3 33.2 - - - +
96A ASN* 5.2 0.5 - - - +
99A ILE* 3.8 22.4 - - - +
100A ARG* 5.2 3.6 - - - +
103A LEU* 4.5 4.0 - - + -
293A SER 4.7 0.2 - - - -
294A VAL* 3.4 1.4 - - - -
295A LEU* 2.9 62.5 + - + +
303A VAL* 1.3 77.3 - - - +
305A ALA* 1.3 63.1 + - - +
306A GLU* 4.2 16.9 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 2.8 12.5 + - - +
71A VAL* 3.4 2.4 - - - -
72A LYS* 2.9 26.9 + - - +
292A THR* 5.9 0.2 - - - +
293A SER 3.6 7.0 - - - +
294A VAL* 4.4 7.6 - - + +
303A VAL* 4.2 2.6 - - + +
304A GLU* 1.3 73.2 - - - +
306A GLU* 1.3 62.7 + - - +
335A ALA* 3.3 30.5 - - - +
338A ARG* 4.3 9.6 - - + -
339A GLY* 4.1 13.5 - - - +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.4 30.3 + - + +
73A CYS 5.8 0.8 - - - -
74A ALA* 5.9 0.3 - - - -
96A ASN* 3.5 23.4 - - - +
100A ARG* 5.3 6.8 + - - -
107A VAL* 5.6 3.1 - - - +
292A THR* 3.5 5.2 + - - -
293A SER* 2.8 51.0 + - - +
295A LEU* 6.0 1.0 - - - +
304A GLU* 4.3 18.3 - - - +
305A ALA* 1.3 78.2 - - - +
307A ALA* 1.3 71.0 + - - +
335A ALA* 3.6 14.4 - - - +
501A NDP 3.9 12.0 + - - -
503A FLC 5.4 1.7 - - - +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 6.1 0.2 - - - -
72A LYS 4.4 2.6 + - - -
74A ALA* 6.1 2.5 - - + +
291A MET 4.2 3.4 - - - -
292A THR* 4.6 0.2 - - - +
293A SER* 4.3 0.6 - - - -
306A GLU* 1.3 91.8 - - - +
308A ALA* 1.3 64.3 + - - +
309A HIS* 3.2 43.6 + - + +
331A ALA* 3.7 23.3 - - + -
332A SER* 3.9 7.2 - - - +
335A ALA* 4.1 4.2 - - - +
501A NDP 4.7 3.3 + - - -
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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