Contacts of the strand formed by residues 720 - 724 (chain A) in PDB entry 2B5L
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 SER 720 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ALA* 3.6 7.7 - - - +
382A PHE* 2.6 40.8 + - - +
719A GLU* 1.3 69.0 - - - +
721A PRO* 1.3 67.8 - - - +
722A ARG* 3.7 19.6 + - - +
737A SER* 3.4 4.4 - - - -
738A SER* 2.9 43.3 + - - -
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Residues in contact with PRO 721 (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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360A VAL* 4.3 11.3 - - - +
378A CYS* 3.8 29.4 - - + +
379A SER 3.7 9.9 - - - +
380A GLY 4.6 4.3 - - - +
385A GLY* 4.0 3.8 - - - -
386A SER 3.5 30.5 - - - +
387A LEU* 4.3 2.5 - - + -
717A LEU* 3.5 19.7 - - + -
719A GLU 3.2 12.3 - - - +
720A SER* 1.3 85.2 - - - +
722A ARG* 1.3 62.5 + - - +
735A VAL* 4.3 5.2 - - + -
736A LEU 3.6 6.1 - - - +
737A SER* 4.5 1.8 - - - -
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Residues in contact with ARG 722 (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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360A VAL* 3.7 25.4 - - - +
361A ASP* 3.8 3.5 - - - +
378A CYS* 4.4 4.5 - - - -
720A SER* 4.0 20.8 - - - +
721A PRO* 1.3 80.1 - - - +
723A LYS* 1.3 81.3 + - + +
736A LEU* 2.7 27.4 + - + +
737A SER* 4.7 2.7 - - - -
738A SER* 3.7 12.5 + - - +
787A GLU* 3.0 28.5 + - - -
789A HIS* 3.4 26.0 + - + +
812A TYR* 5.1 0.2 - - - -
813A ALA 4.6 9.1 + - - +
814A LEU* 5.3 4.0 - - - +
28C THR* 3.4 35.3 + - - +
31C GLN* 5.0 5.1 - - - +
32C VAL* 5.9 4.3 - - - +
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Residues in contact with LYS 723 (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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360A VAL 4.3 7.1 + - - -
361A ASP* 3.2 19.0 + - - +
378A CYS* 3.6 2.8 - - - -
722A ARG* 1.3 87.8 + - + +
724A ILE* 1.3 68.8 + - - +
735A VAL* 3.3 9.0 - - - +
736A LEU* 3.1 43.0 + - + -
814A LEU 3.5 26.7 - - - +
815A SER* 5.2 1.1 - - - +
816A LEU* 4.0 15.5 - - + +
871A TYR 5.7 1.6 - - - -
1005A ASN 5.5 2.8 + - - -
27C PHE* 5.7 7.3 - - - -
31C GLN* 4.0 25.0 - - - +
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Residues in contact with ILE 724 (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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361A ASP* 3.1 21.0 + - - +
362A MET* 4.1 20.6 - - - +
363A CYS* 4.3 13.3 - - - +
376A VAL* 4.0 31.2 - - + +
378A CYS* 3.7 19.1 - - - -
387A LEU* 4.5 9.2 - - + -
723A LYS* 1.3 82.3 - - - +
725A CYS* 1.3 80.1 + - - +
733A PHE* 4.1 13.0 - - + -
734A GLY 3.1 11.4 - - - +
735A VAL* 3.7 15.9 - - + -
816A LEU* 3.9 1.6 - - - +
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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