Contacts of the strand formed by residues 122 - 125 (chain X) in PDB entry 2AW2
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 ASN 122 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X ASN* 3.6 5.2 - - - +
119X PHE* 2.7 56.8 + - + +
120X GLN 2.8 13.9 + - - +
121X SER* 1.3 80.4 - - - +
123X LEU* 1.3 59.4 + - - +
23Y TYR* 4.8 0.2 - - - -
26Y LYS* 3.4 32.6 + - - +
36Y VAL* 4.5 5.9 - - + +
37Y CYS 3.5 12.2 + - - +
38Y GLU* 4.2 10.3 + - - +
39Y PRO* 3.9 15.2 - - - +
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Residues in contact with LEU 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X SER* 4.4 13.0 - - - +
117X ALA 3.4 14.6 - - - +
118X ASN* 3.2 33.7 - - - +
122X ASN* 1.3 77.3 - - - +
124X ILE* 1.3 62.5 + - - +
125X GLU* 3.2 33.2 - - + +
20Y SER* 3.3 17.5 - - - +
23Y TYR* 3.9 31.2 - - + -
36Y VAL* 3.5 2.1 - - - +
37Y CYS* 2.5 43.7 + - + +
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Residues in contact with ILE 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36X VAL* 3.2 42.0 - - + +
37X GLN* 3.6 24.7 - - - +
38X LEU* 3.6 24.5 - - + +
116X SER* 3.2 7.1 - - - -
117X ALA* 3.0 38.9 + - + +
119X PHE* 3.5 28.0 - - + -
123X LEU* 1.3 76.7 - - - +
125X GLU* 1.3 64.4 + - - +
34Y GLY 4.7 0.2 - - - -
35Y THR 3.4 5.4 - - - +
36Y VAL* 4.2 19.3 - - + -
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Residues in contact with GLU 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114X ARG* 3.4 21.0 - - - -
115X CYS 4.3 0.2 - - - -
116X SER* 3.2 24.7 - - - -
123X LEU* 3.2 13.9 - - + +
124X ILE* 1.3 72.8 - - - +
126X SER* 1.3 63.5 + - - +
17Y PRO* 3.6 12.6 - - + +
18Y LYS 4.0 18.2 - - - +
20Y SER* 2.5 32.1 + - - -
34Y GLY* 4.1 1.6 - - - -
35Y THR* 2.7 41.2 + - - +
37Y CYS* 3.9 22.0 - - - -
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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
------------------------------------------------------------
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