Contacts of the strand formed by residues 5 - 10 (chain X) in PDB entry 2BQ8
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 5 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4X ALA* 1.3 74.2 - - - +
6X ARG* 1.3 59.4 + - - +
7X PHE* 4.9 2.6 - - + -
43X ASP* 3.5 24.0 - - + +
44X PHE* 3.7 28.5 - - + -
120X PHE* 3.7 33.2 - - + -
121X LYS 4.4 13.9 - - - +
122X ILE* 3.8 14.8 - - + +
123X PRO* 4.9 4.7 - - + -
129X VAL* 4.0 23.1 - - + -
274X VAL 3.7 1.0 - - - +
275X GLU* 3.3 3.8 - - - -
276X ILE* 2.8 44.3 + - + +
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Residues in contact with ARG 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X ALA* 5.3 9.6 - - - +
2X THR* 3.6 19.4 + - - +
4X ALA* 3.5 33.1 + - + +
5X LEU* 1.3 79.0 - - - +
7X PHE* 1.3 63.7 + - - +
40X LEU 3.6 18.5 + - - -
41X GLY* 3.7 19.5 - - - +
42X ALA* 3.9 3.4 - - - -
43X ASP* 2.6 48.1 + - - +
44X PHE* 4.4 0.5 - - - -
273X TYR* 3.5 17.0 + - - +
274X VAL 3.3 5.2 - - - +
275X GLU* 4.0 23.9 + - + -
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Residues in contact with PHE 7 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X LEU* 4.9 4.7 - - + -
6X ARG* 1.3 77.9 - - - +
8X VAL* 1.3 74.9 + - - +
9X ALA* 4.2 3.1 - - + -
42X ALA* 4.5 2.5 - - - -
44X PHE* 3.1 54.5 - + + +
46X LEU* 3.6 22.9 - - + -
131X ILE* 4.5 1.8 - - + -
180X LEU* 3.7 21.1 - - + -
216X LEU* 3.8 10.8 - - + -
273X TYR* 3.6 6.2 - - - -
274X VAL* 2.7 82.3 + - + -
276X ILE* 4.0 16.4 - - + -
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Residues in contact with VAL 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X PHE* 1.3 80.9 - - - +
9X ALA* 1.3 68.0 + - - +
10X VAL* 4.3 4.0 - - + +
33X ILE* 4.0 36.6 - - + -
36X THR* 4.6 5.6 - - + -
37X VAL* 4.7 10.5 - - + -
42X ALA* 4.8 1.5 - - + +
44X PHE 3.4 4.9 + - - -
45X ILE* 3.4 15.4 - - + -
46X LEU 2.8 27.2 + - - +
271X PHE* 3.8 29.2 - - + -
272X ALA 3.3 3.6 - - - -
273X TYR* 4.1 18.2 - - + -
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Residues in contact with ALA 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X PHE* 4.0 9.1 + - + -
8X VAL* 1.3 74.5 - - - +
10X VAL* 1.3 59.5 + - - +
46X LEU* 3.5 9.0 - - + +
48X LEU* 4.0 19.3 - - + -
216X LEU* 4.0 22.2 - - + -
235X VAL* 5.5 0.7 - - + -
237X SER* 2.9 20.1 + - - +
271X PHE* 3.7 0.9 - - - +
272X ALA* 2.8 33.6 + - + +
274X VAL* 5.0 1.3 - - + -
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Residues in contact with VAL 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X VAL* 4.3 1.1 - - + -
9X ALA* 1.3 74.8 - - - +
11X GLY* 1.3 62.7 + - - +
13X TRP* 4.0 23.1 - - + +
29X ASN* 5.2 3.6 - - + -
33X ILE* 4.1 29.2 - - + -
45X ILE* 4.2 17.9 - - + -
46X LEU 3.0 13.5 + - - +
47X SER* 3.3 4.0 - - - -
48X LEU* 2.9 23.5 + - - +
73X PHE* 5.6 2.5 - - + -
83X TRP* 4.4 9.9 - - + -
237X SER* 3.9 3.8 - - - -
240X GLY* 3.9 24.2 - - - +
270X GLY 4.7 0.9 - - - +
271X PHE* 4.2 10.8 - - + -
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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