Contacts of the strand formed by residues 624 - 628 (chain B) in PDB entry 5FWP
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 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B LYS 4.8 12.8 - - - +
575B VAL* 3.4 3.2 - - + +
576B GLU* 2.8 36.7 + - + +
591B ILE* 3.7 23.1 - - + -
592B VAL 3.5 2.9 - - - -
593B THR* 6.2 0.2 - - - -
598B TRP 5.3 1.1 + - - -
603B GLU* 3.1 28.6 + - - -
621B MET* 4.7 7.1 - - - +
622B ALA* 2.9 27.6 + - - +
623B LYS* 1.3 71.8 - - - +
625B HIS* 1.3 64.3 + - - +
659B PHE* 5.7 0.7 - - + -
663B LEU* 4.6 7.9 - - + -
668B PHE* 3.5 33.9 - - + -
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Residues in contact with HIS 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B GLU* 3.7 24.1 + - + -
575B VAL* 3.7 2.7 - - - -
576B GLU* 3.6 20.9 - - + -
577B LYS* 3.3 38.4 + - + +
579B THR* 5.7 3.6 - - + -
590B CYS 3.5 0.3 - - - +
591B ILE* 3.3 8.3 - - - -
592B VAL* 3.0 51.0 + - + +
594B SER* 4.1 8.6 - - - -
623B LYS* 3.6 31.5 + - + +
624B LYS* 1.3 76.7 + - - +
626B LEU* 1.3 62.2 + - - +
627B GLU* 3.5 3.9 + - - +
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Residues in contact with LEU 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B MET* 4.4 15.5 - - + -
571B LEU* 4.8 10.3 - - + -
575B VAL* 3.3 15.5 - - + +
577B LYS 2.7 10.7 + - - +
578B VAL* 4.0 25.4 - - + -
579B THR* 2.9 27.9 + - - +
589B CYS* 3.8 30.3 - - + -
590B CYS 4.1 2.5 - - - +
591B ILE* 3.5 21.8 - - + -
625B HIS* 1.3 69.8 - - - +
627B GLU* 1.3 65.7 + - - +
628B ILE* 3.8 6.0 + - + +
655B VAL* 5.7 1.8 - - + +
659B PHE* 4.3 18.2 - - + -
662B ALA* 4.5 2.2 - - + -
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Residues in contact with GLU 627 (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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539B GLU* 5.1 2.1 - - - +
579B THR* 3.4 23.4 - - - +
581B SER* 3.1 26.8 - - - -
583B ARG* 3.5 24.0 + - - +
584B LEU* 3.8 17.9 - - + -
589B CYS* 3.0 9.0 - - - +
590B CYS* 2.7 37.0 + - + +
592B VAL* 3.4 40.1 - - + +
625B HIS* 5.0 1.9 - - - +
626B LEU* 1.3 74.1 - - - +
628B ILE* 1.3 61.0 + - - +
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Residues in contact with ILE 628 (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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560B PHE* 5.8 0.4 - - + -
563B LEU* 5.6 1.6 - - + -
564B CYS* 3.7 17.3 - - - -
567B MET* 3.4 35.0 - - + -
578B VAL* 3.5 18.2 - - + -
579B THR 2.7 14.6 + - - +
580B ILE* 3.0 18.5 - - + +
581B SER 2.8 27.8 + - - +
584B LEU* 4.1 2.9 - - - -
588B PRO 3.6 4.3 - - - +
589B CYS* 4.7 2.9 - - + -
626B LEU* 4.1 11.0 - - + +
627B GLU* 1.3 79.4 - - - +
629B ASN* 1.3 64.2 + - - +
630B PRO* 3.2 3.3 - - - +
635B VAL* 3.5 37.2 - - + -
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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
------------------------------------------------------------
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