Contacts of the strand formed by residues 269 - 273 (chain D) in PDB entry 3GEB
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 ARG 269 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A MET* 3.6 15.0 - - - +
269A ARG* 5.9 0.6 - - - +
496A VAL* 3.2 33.3 - - - +
268D GLU* 1.3 79.7 + - - +
270D VAL* 1.3 66.9 + - - +
271D PHE* 3.9 17.3 - - + -
438D ARG* 4.8 1.9 - - - +
440D ASN 3.0 6.7 + - - +
441D CYS* 3.2 20.5 - - - -
442D VAL* 3.1 23.8 + - - +
496D VAL* 3.3 29.6 - - + +
498D VAL* 4.8 5.4 - - + -
536D GLU 4.7 3.4 + - - -
537D TYR 4.5 3.8 + - - -
538D LEU* 2.4 51.0 + - - +
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D GLU* 4.7 4.3 - - - +
269D ARG* 1.3 80.0 - - - +
271D PHE* 1.3 62.5 + - - +
272D VAL* 3.6 5.6 + - + +
442D VAL* 3.7 19.7 - - + -
444D VAL* 4.0 11.7 - - + -
487D ILE* 4.3 3.4 - - + -
491D PHE* 3.8 45.1 - - + -
495D ALA* 4.0 11.7 - - + -
496D VAL 3.0 6.5 + - - -
497D TYR* 3.3 32.9 - - + +
498D VAL* 2.9 24.0 + - - -
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Residues in contact with PHE 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ARG* 3.9 24.7 - - + -
270D VAL* 1.3 71.9 - - - +
272D VAL* 1.3 60.8 + - - +
273D TRP* 3.3 20.1 - - - +
435D ILE* 3.4 37.7 - - + -
438D ARG* 3.9 9.6 - - - -
441D CYS* 4.0 8.5 - - + -
442D VAL 2.9 14.0 + - - +
443D ASN* 4.0 0.4 - - - +
444D VAL* 2.9 29.3 + - - +
498D VAL* 3.3 37.0 - - + +
500D ILE* 3.9 13.9 - - + -
533D LEU* 3.9 18.6 - - + -
538D LEU* 3.7 27.8 - - + -
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D VAL* 4.0 21.1 - - + +
271D PHE* 1.3 74.1 - - - +
273D TRP* 1.3 60.1 + - - +
444D VAL* 3.6 7.6 - - + -
446D VAL* 3.5 33.2 - - + -
484D PHE* 3.8 22.4 - - + -
487D ILE* 4.0 19.1 - - + -
497D TYR* 4.6 12.6 - - + -
498D VAL 2.8 11.6 + - - +
499D VAL* 3.5 14.2 - - + +
500D ILE* 3.0 25.1 + - - +
515D MET* 5.8 1.6 - - - -
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Residues in contact with TRP 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D PHE* 3.3 19.0 - - - +
272D VAL* 1.3 74.7 - - - +
274D ASP* 1.3 61.5 + - - +
278D THR* 4.2 8.1 - - + -
279D ILE* 3.7 37.9 - - + -
428D SER* 5.4 4.9 - - - -
431D ALA* 4.0 23.1 - - + -
432D LEU* 3.4 17.7 - - + +
435D ILE* 3.5 24.9 - - + -
443D ASN* 2.8 22.7 + - + -
444D VAL 2.8 18.7 + - - +
445D LEU* 3.6 4.3 - - + +
446D VAL* 2.9 30.8 + - - +
467D PHE* 4.0 10.3 - + - -
500D ILE* 3.7 39.9 - - + -
520D ILE* 5.2 1.1 - - + -
526D LEU* 5.7 2.9 - - + -
529D LEU* 4.0 17.3 - - + -
533D LEU* 4.9 0.4 - - + -
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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