Contacts of the strand formed by residues 638 - 646 (chain B) in PDB entry 4XUF
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 SER 638 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628B THR* 4.0 13.0 - - - +
629B ALA 3.4 8.3 - - - -
630B TYR* 3.2 40.6 + - - -
636B GLY 3.6 2.6 + - - -
637B VAL* 1.3 81.9 - - - +
639B ILE* 1.3 61.0 + - - +
640B GLN* 5.9 0.7 + - - -
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Residues in contact with ILE 639 (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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628B THR* 3.6 5.4 - - - -
629B ALA 3.2 27.3 + - - -
632B ILE* 3.3 32.1 - - + -
633B SER* 3.9 14.4 - - - -
634B LYS* 4.7 18.6 - - + +
637B VAL* 3.5 19.3 + - + +
638B SER* 1.3 79.3 - - - +
640B GLN* 1.3 69.1 + - - +
641B VAL* 3.7 17.3 - - + -
678B LEU* 3.8 15.0 - - + -
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Residues in contact with GLN 640 (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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626B ASN* 3.3 22.2 - - - +
627B ALA 3.4 6.8 - - - +
628B THR* 3.6 20.2 + - - +
638B SER 5.9 0.6 + - - -
639B ILE* 1.3 82.4 - - - +
641B VAL* 1.3 64.3 + - - +
692B GLU* 5.3 0.2 - - - -
693B TYR* 3.2 39.9 + - + +
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Residues in contact with VAL 641 (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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610B LEU* 4.6 0.7 - - + -
626B ASN* 3.4 7.8 - - - +
627B ALA* 2.9 58.3 + - + +
629B ALA* 3.9 21.3 - - + -
632B ILE* 4.3 1.1 - - + -
639B ILE* 3.7 25.6 - - + -
640B GLN* 1.3 81.0 - - - +
642B ALA* 1.3 59.9 + - - +
643B VAL* 4.3 4.5 - - + -
678B LEU* 3.8 8.5 - - + -
690B ILE* 3.7 20.2 - - + -
691B PHE 3.5 14.6 - - - +
693B TYR* 3.9 8.3 - - - -
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Residues in contact with ALA 642 (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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616B LEU* 5.0 1.3 - - + -
624B VAL* 4.3 9.0 - - + -
625B MET 3.5 4.9 - - - +
626B ASN* 5.0 0.4 - - - +
641B VAL* 1.3 73.9 - - - +
643B VAL* 1.3 60.9 + - - +
689B LEU 3.1 3.8 - - - +
690B ILE* 3.5 0.7 - - - -
691B PHE* 2.7 47.2 + - + +
692B GLU 4.6 3.8 - - - +
693B TYR* 4.4 3.9 - - + +
1001B P30 3.6 40.6 - - + +
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Residues in contact with VAL 643 (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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610B LEU* 4.3 10.5 - - + -
612B PHE* 4.1 10.3 - - + -
624B VAL* 3.4 4.7 - - - -
625B MET 2.9 35.2 + - - +
627B ALA* 3.7 28.3 - - + -
641B VAL* 4.3 8.5 - - + -
642B ALA* 1.3 75.9 - - - +
644B LYS* 1.3 61.3 + - - +
645B MET* 3.7 27.1 - - + +
688B TYR* 3.7 33.0 - - + -
689B LEU 3.3 4.7 - - - +
690B ILE* 4.4 7.4 - - + -
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Residues in contact with LYS 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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623B LYS 3.7 4.3 - - - +
624B VAL* 4.0 15.5 - - + -
642B ALA 4.0 0.4 + - - -
643B VAL* 1.3 71.3 - - - +
645B MET* 1.3 66.1 + - - +
658B LEU* 4.2 15.0 - - + +
661B GLU* 2.6 43.7 + - - +
687B ILE 3.5 5.5 - - - +
688B TYR 3.8 0.2 - - - -
689B LEU* 2.9 47.2 + - + +
691B PHE* 4.6 6.7 - - + -
829B ASP 3.4 11.5 + - - -
831B GLY* 4.0 1.6 - - - +
832B LEU* 3.9 34.7 - - + +
833B ALA* 4.4 8.7 - - - +
1001B P30 3.3 23.3 + - + +
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Residues in contact with MET 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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612B PHE* 3.6 31.9 - - + -
622B GLY* 3.4 3.8 - - - -
623B LYS* 2.9 49.0 + - + +
625B MET* 3.9 27.1 - - + +
643B VAL* 3.7 28.5 - - + +
644B LYS* 1.3 77.8 - - - +
646B LEU* 1.3 73.4 + - - +
658B LEU* 4.2 4.3 - - - +
686B PRO* 5.6 1.6 - - + -
687B ILE 3.8 7.0 - - - +
688B TYR* 3.7 29.4 - - + -
832B LEU* 5.6 0.9 - - - +
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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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621B PHE 3.6 15.5 - - - +
622B GLY* 4.2 5.2 - - - -
623B LYS* 5.1 1.2 - - - -
645B MET* 1.3 88.7 - - - +
647B LYS* 1.3 62.3 + - - +
650B ALA* 3.9 10.8 - - + -
654B GLU* 3.8 18.4 - - + +
655B ARG* 3.8 42.0 - - + +
658B LEU* 3.5 34.8 - - + -
686B PRO* 5.1 12.9 - - + +
687B ILE* 4.7 8.5 + - + +
832B LEU* 4.5 4.5 - - + -
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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