Contacts of the strand formed by residues 28 - 33 (chain B) in PDB entry 2XGZ
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 GLY 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B THR* 3.5 3.5 - - - -
25B THR 3.0 33.2 + - - +
26B GLU 3.3 1.6 - - - -
27B LYS* 1.3 80.0 - - - +
29B VAL* 1.3 65.0 + - - -
30B PHE* 3.3 10.9 - - - -
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Residues in contact with VAL 29 (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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22B GLU* 3.8 41.1 - - + +
23B LEU 3.7 2.7 - - - +
24B THR* 3.9 23.3 - - + +
28B GLY* 1.3 73.7 - - - -
30B PHE* 1.3 71.8 + - - +
31B ARG* 4.3 1.6 + - + +
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Residues in contact with PHE 30 (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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22B GLU* 3.2 3.5 - - - -
23B LEU 2.8 45.3 + - - +
25B THR* 3.5 17.9 - - - -
27B LYS* 3.7 19.5 - - + -
28B GLY* 3.3 21.3 - - - -
29B VAL* 1.3 79.2 - - - +
31B ARG* 1.3 60.4 + - - +
116B ALA* 3.7 25.9 - - - +
119B ARG* 3.9 20.0 - - + +
120B ALA* 3.6 20.2 - - + +
123B ALA* 3.4 35.0 - - + -
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Residues in contact with ARG 31 (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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411A GLN* 4.7 3.4 + - - -
414A ARG* 3.4 39.7 - - - +
20B GLU* 3.3 37.2 + - + +
21B VAL 3.2 5.6 - - - +
22B GLU* 3.1 29.6 + - + -
29B VAL* 4.3 2.2 + - + +
30B PHE* 1.3 75.6 - - - +
32B SER* 1.3 65.9 + - - +
33B ILE* 4.6 5.4 - - + -
116B ALA* 4.6 0.9 - - - -
119B ARG* 2.8 30.8 + - - +
380B ASP* 4.7 0.2 - - - -
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Residues in contact with SER 32 (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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19B VAL 4.1 0.3 - - - +
20B GLU* 3.3 3.5 - - - +
21B VAL 2.8 32.3 + - - +
31B ARG* 1.3 75.6 - - - +
33B ILE* 1.3 67.3 + - - +
34B VAL* 4.8 0.8 - - - +
112B GLY* 3.5 28.6 + - - -
115B LEU* 3.2 31.1 - - - +
116B ALA* 3.7 13.0 - - - -
119B ARG* 3.7 2.0 + - - +
380B ASP* 3.5 8.0 + - - -
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Residues in contact with ILE 33 (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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414A ARG* 4.0 3.1 - - - +
10B VAL* 3.5 27.4 - - + -
11B TYR 5.8 0.2 - - - +
18B THR* 3.7 3.6 - - + -
19B VAL 3.6 8.1 - - - +
20B GLU* 3.3 26.9 - - - +
31B ARG* 4.6 6.5 - - + -
32B SER* 1.3 80.7 + - - +
34B VAL* 1.3 65.5 + - - +
35B PRO* 3.9 4.9 - - - +
115B LEU* 5.1 3.6 - - - +
378B THR* 3.7 29.6 + - + +
379B GLU* 3.8 37.9 - - + +
380B ASP* 2.9 31.6 + - + +
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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