Contacts of the strand formed by residues 643 - 648 (chain B) in PDB entry 3GUT
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 LYS 643 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549B LYS* 5.9 2.4 - - - +
550B ILE* 3.8 42.8 + - + -
551B VAL 5.3 3.6 - - - -
552B ARG* 6.5 0.4 - - - -
553B MET* 4.6 15.0 - - + -
556B THR* 5.6 5.6 - - + -
628B PHE* 4.2 3.3 - - - -
629B VAL* 2.9 46.8 + - + +
641B GLU* 3.0 15.8 + - - +
642B PRO* 1.3 75.6 + - - +
644B PRO* 1.4 80.0 - - + +
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Residues in contact with PRO 644 (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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553B MET* 6.0 0.3 - - - +
556B THR* 3.8 18.0 - - - +
626B SER* 6.6 0.2 - - - -
627B VAL 3.8 8.7 - - - +
628B PHE* 4.3 15.5 - - + -
629B VAL* 5.0 1.2 - - - +
642B PRO 4.1 4.7 - - - +
643B LYS* 1.4 97.4 - - + +
645B PHE* 1.3 59.8 + - - +
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Residues in contact with PHE 645 (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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553B MET* 4.8 10.1 - - + -
555B ARG 4.1 9.2 - - - -
556B THR* 3.0 26.2 - - - -
557B ALA 3.7 3.8 - - - -
558B GLY* 3.6 28.5 - - - -
566B ILE* 5.2 5.2 - - + -
582B PHE* 3.7 23.6 - + + -
611B PHE* 6.1 0.2 - + - -
613B THR* 3.7 21.5 - - - -
626B SER* 3.7 3.4 - - - -
627B VAL* 2.9 55.3 + - + +
629B VAL* 4.3 16.2 - - + -
643B LYS 3.7 0.9 + - - +
644B PRO* 1.3 74.2 - - - +
646B LEU* 1.3 63.8 + - - +
647B TYR* 3.9 26.0 - + - -
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Residues in contact with LEU 646 (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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556B THR 2.8 10.2 + - - +
557B ALA* 2.9 17.6 - - + +
558B GLY 2.6 34.4 + - - +
624B PRO* 3.5 27.8 - - + -
625B ALA 3.3 19.7 - - - +
626B SER* 3.3 26.2 - - - +
645B PHE* 1.3 76.0 - - - +
647B TYR* 1.3 60.5 - - - +
648B TYR* 3.5 13.4 + - + +
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Residues in contact with TYR 647 (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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558B GLY 3.1 6.1 - - - -
559B CYS 2.9 33.0 - - - -
560B VAL* 3.6 23.5 - - + +
582B PHE* 4.6 4.9 - + - -
592B TRP* 4.0 20.0 - + - -
613B THR* 2.9 21.8 - - + +
614B PRO* 2.7 38.4 + - - +
616B TYR* 3.8 24.2 - + + -
621B ILE* 4.7 0.5 - - - +
624B PRO* 3.3 1.6 - - - +
625B ALA* 2.9 39.2 + - + +
627B VAL* 3.5 29.4 - - + -
645B PHE* 3.9 14.0 + + - -
646B LEU* 1.3 71.4 - - - +
648B TYR* 1.3 61.9 + - - +
649B PRO* 4.2 0.3 - - - +
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Residues in contact with TYR 648 (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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555B ARG* 3.3 32.5 + - - -
557B ALA* 4.0 4.7 - - + -
558B GLY 2.9 21.6 + - - -
559B CYS* 3.2 22.6 + - + -
560B VAL* 3.1 21.6 + - - -
564B GLU* 3.3 18.5 + - - -
624B PRO* 3.9 7.9 - - + -
646B LEU* 3.5 19.7 - - + +
647B TYR* 1.3 73.0 - - - +
649B PRO* 1.3 79.6 - - + +
650B GLU* 5.8 0.9 - - + -
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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