Contacts of the strand formed by residues 445 - 448 (chain P) in PDB entry 2GLJ
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 GLU 445 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109P PRO* 5.9 0.4 - - - +
260P MET* 3.1 5.2 - - - -
261P GLY 2.9 29.6 + - - +
263P GLY* 3.3 10.9 + - - -
264P GLN* 2.8 47.1 + - + +
265P ASP* 3.0 26.8 + - - +
437P LEU* 3.9 7.0 - - + +
438P LEU 4.0 3.6 - - - +
439P ASN* 3.5 20.2 - - - +
440P MSE 3.7 5.0 - - - -
441P HIS* 3.1 23.8 + - - -
442P ALA 3.5 15.7 - - - +
444P TRP* 1.3 72.5 - - - +
446P ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 446 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLY 6.1 0.7 - - - -
174M VAL 6.6 0.2 - - - -
175M SER* 5.9 2.5 - - - -
200M ASN* 4.6 1.6 - - - +
252P TYR* 3.6 37.7 - - + +
258P MET* 3.6 39.9 - - + -
259P VAL 3.2 5.2 - - - +
260P MET* 4.1 20.6 - - + -
264P GLN* 4.2 0.2 - - - -
363P LEU* 5.1 1.8 - - + +
437P LEU* 3.1 19.1 - - - +
438P LEU* 3.1 46.0 + - + +
439P ASN* 4.4 10.8 - - - +
445P GLU* 1.3 79.1 - - - +
447P SER* 1.3 65.7 + - - +
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Residues in contact with SER 447 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN* 5.1 0.2 + - - -
258P MET* 3.0 10.8 - - - -
259P VAL* 2.8 38.8 + - - +
264P GLN* 2.8 33.4 + - - -
268P ILE* 3.7 16.8 - - - +
363P LEU* 4.3 2.9 - - - -
435P VAL* 4.9 1.6 - - - -
436P ALA 4.4 5.4 - - - -
437P LEU* 3.5 11.4 - - - -
446P ILE* 1.3 75.9 - - - +
448P SER* 1.3 61.6 + - - +
449P LYS 3.7 0.2 + - - -
452P ILE* 3.9 5.8 - - - +
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Residues in contact with SER 448 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M ILE* 4.7 3.2 - - - +
13P TRP* 4.3 5.7 + - - -
257P SER 3.8 7.4 + - - -
258P MET* 4.3 1.6 - - - -
363P LEU* 3.4 22.5 - - - +
364P GLY* 3.8 7.5 - - - -
435P VAL* 5.1 0.2 - - - +
436P ALA 4.7 2.8 + - - -
447P SER* 1.3 72.5 - - - +
449P LYS* 1.3 67.1 + - - +
450P ALA* 3.4 16.3 + - - +
451P ASP* 2.8 42.6 + - - +
452P ILE* 2.9 15.3 + - - +
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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