Contacts of the strand formed by residues 557 - 561 (chain B) in PDB entry 1GPU
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 ILE 557 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B PRO* 3.2 4.6 - - - +
556B ASP* 1.3 82.7 - - - +
558B ILE* 1.3 73.6 + - - +
559B LEU* 4.3 5.2 - - + -
576B LEU* 4.6 9.9 - - + -
581B ILE* 5.0 0.4 - - + -
582B LYS 3.3 3.5 + - - +
583B ALA* 3.3 22.2 - - + -
584B ARG 3.0 23.2 + - - -
610B VAL* 3.8 3.8 - - - -
611B PRO* 3.4 18.2 - - + +
613B MET* 4.0 20.0 - - + -
660B ALA* 3.7 36.3 - - + +
663B THR* 4.1 12.1 - - + -
664B ILE* 4.0 15.5 - - + -
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Residues in contact with ILE 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B PRO* 4.7 2.5 - - + -
557B ILE* 1.3 79.7 - - - +
559B LEU* 1.3 68.9 + - - +
560B VAL 3.8 0.6 + - - +
584B ARG* 3.4 30.7 - - + +
586B VAL* 3.8 25.8 - - + -
605B VAL 3.9 7.9 - - - +
606B LEU* 4.5 3.1 - - + -
607B PRO* 3.8 23.1 - - + -
610B VAL* 3.7 30.3 - - + -
611B PRO 2.9 12.2 + - - +
612B ILE* 3.4 19.9 - - + -
613B MET 3.0 27.2 + - - +
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Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE* 4.3 7.9 - - + -
558B ILE* 1.3 77.5 - - - +
560B VAL* 1.3 59.4 + - - +
561B ALA 4.0 0.4 + - - -
569B SER* 3.7 42.0 - - - +
572B ALA* 4.3 14.1 - - + -
573B ALA 4.6 0.7 - - - +
576B LEU* 4.4 5.8 - - + -
583B ALA* 4.3 23.8 - - + -
584B ARG 2.8 11.7 + - - +
585B VAL* 3.5 8.1 - - + +
586B VAL 2.8 27.5 + - - +
613B MET* 3.5 34.1 - - + +
615B VAL* 4.7 1.8 - - + -
656B VAL* 4.4 4.3 - - + -
660B ALA* 4.2 14.4 - - + -
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Residues in contact with VAL 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B ILE* 3.8 1.3 + - + -
559B LEU* 1.3 72.1 - - - +
561B ALA* 1.3 63.0 + - - +
586B VAL* 3.4 28.7 - - + +
588B LEU* 4.0 17.5 - - + -
606B LEU* 4.6 7.9 - - + -
612B ILE* 3.8 23.8 - - + -
613B MET 3.0 5.8 + - - +
614B SER* 3.1 24.9 - - - -
615B VAL* 2.8 24.7 + - - +
623B TRP* 4.0 19.3 - - + -
626B TYR* 5.1 4.3 - - + +
627B ALA* 4.2 3.1 - - + -
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Residues in contact with ALA 561 (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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559B LEU 4.0 0.4 + - - +
560B VAL* 1.3 75.2 - - - +
562B THR* 1.3 67.7 + - - +
565B GLU 3.6 26.5 - - - +
566B VAL* 3.8 8.5 - - + +
569B SER* 3.6 13.7 - - - +
585B VAL* 6.0 0.4 - - + -
586B VAL 3.0 8.4 + - - +
587B SER* 3.5 5.5 - - - -
588B LEU* 2.9 25.8 + - - +
615B VAL* 3.1 19.3 - - + +
623B TRP* 4.8 1.8 - - - -
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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