Contacts of the strand formed by residues 302 - 305 (chain A) in PDB entry 6A08
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 ALA 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.9 12.6 - - + -
64A ILE* 4.3 5.4 - - + -
72A PRO* 3.3 23.8 - - - +
73A MET* 4.1 3.1 - - - +
124A TRP* 6.2 1.1 - - + -
280A VAL 4.1 0.2 + - - -
281A LEU* 3.2 41.7 - - + +
282A VAL 3.2 4.0 + - - -
296A THR* 5.9 1.6 - - - -
300A ALA* 3.3 7.9 - - - +
301A SER* 1.3 81.5 - - - +
303A VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO 3.0 18.3 + - - +
73A MET* 3.2 17.7 - - + -
74A ALA 2.9 23.7 + - - -
281A LEU* 4.8 0.2 - - - -
282A VAL* 3.2 14.4 - - + +
286A ILE* 4.1 16.8 - - + -
292A VAL* 4.1 26.2 - - + +
295A ALA* 3.5 31.6 - - + -
296A THR* 5.6 1.1 - - - +
300A ALA* 5.1 0.4 - - + -
302A ALA* 1.3 81.0 - - - +
304A LEU* 1.3 67.5 + - - +
305A VAL* 4.2 9.9 - - + -
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Residues in contact with LEU 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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74A ALA* 3.3 23.1 - - + +
75A VAL 5.0 0.9 - - - +
76A ALA* 3.8 12.3 - - + -
77A PRO* 4.1 14.4 - - + -
104A THR* 5.2 1.8 - - - +
124A TRP* 4.3 6.7 - - + -
152A VAL* 5.6 2.0 - - + -
228A LYS* 4.0 16.4 - - + -
248A VAL* 3.8 30.1 - - + -
281A LEU* 3.8 20.9 - - + -
282A VAL 3.0 6.7 + - - -
283A ASP* 3.5 28.9 - - + +
286A ILE* 4.0 4.0 - - - +
303A VAL* 1.3 82.2 - - - +
305A VAL* 1.3 59.6 + - - +
306A GLY 4.3 0.2 - - - -
401A MG 2.8 25.5 - - - -
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Residues in contact with VAL 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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6A LEU* 5.0 0.7 - - + -
73A MET* 3.9 31.2 - - + -
74A ALA 3.1 8.4 + - - +
75A VAL* 3.8 2.1 - - - +
76A ALA* 2.9 20.0 + - - -
286A ILE* 4.0 29.6 - - + +
303A VAL* 4.2 2.0 - - + -
304A LEU* 1.3 80.3 - - - +
306A GLY* 1.3 59.9 + - - +
308A PRO* 3.8 33.2 - - + -
309A VAL* 3.6 24.8 - - + +
328A LEU* 4.8 11.0 - - + -
401A MG 4.0 0.4 - - - -
402A FMN 3.9 2.0 - - - -
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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