Contacts of the strand formed by residues 641 - 646 (chain A) in PDB entry 6F3T
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 TYR 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A LYS 4.2 3.5 + - - -
372A VAL* 3.6 23.7 - - + -
373A PHE* 3.0 60.8 + - + -
374A PHE* 5.4 0.4 - - - -
426A ARG* 3.7 13.5 + - - -
635A PHE* 3.7 3.8 - - - -
636A HIS* 2.9 39.7 + + + +
638A ASN* 3.9 6.1 + - - -
639A SER 3.4 0.4 - - - -
640A ASN* 1.3 95.8 - - + +
642A VAL* 1.3 67.3 + - - +
653A LEU* 4.1 12.6 - - + -
654A TRP 3.2 17.5 - - - +
655A ASP* 3.8 18.4 + - - -
656A VAL* 4.2 1.6 - - - -
662A VAL* 4.0 22.7 - - + -
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Residues in contact with VAL 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A VAL* 4.1 21.3 - - + -
611A LEU* 4.4 2.0 - - + -
623A PHE* 4.1 25.8 - - + -
633A THR* 5.0 0.2 - - - -
634A ARG 3.4 10.3 - - - +
635A PHE* 3.6 39.9 - - + -
641A TYR* 1.3 75.2 - - - +
643A ALA* 1.3 73.0 + - - +
644A THR* 4.3 9.4 - - + -
653A LEU* 3.3 4.4 - - - -
654A TRP* 2.6 42.0 + - + +
656A VAL* 4.0 9.6 - - + +
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Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A THR* 3.4 5.2 - - - -
634A ARG 2.8 31.6 + - - +
642A VAL* 1.3 74.3 - - - +
644A THR* 1.3 62.3 + - - +
651A VAL* 5.0 0.4 - - + -
652A ARG 3.1 9.4 - - - +
653A LEU* 3.9 7.4 - - + +
675A LEU* 3.6 22.3 - - + +
677A PHE* 3.5 26.2 - - + -
684A LEU* 4.3 10.8 - - + -
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Residues in contact with THR 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A ALA* 3.8 27.8 - - + -
626A HIS* 2.7 30.2 + - + -
630A VAL* 4.2 7.9 - - + -
632A CYS 3.2 10.5 - - - +
633A THR* 4.1 3.1 - - + -
642A VAL* 4.3 4.9 - - + -
643A ALA* 1.3 79.3 - - - +
645A GLY* 1.3 59.4 + - - +
650A THR 4.1 0.7 - - - +
651A VAL* 3.3 8.3 - - - +
652A ARG* 2.8 32.2 + - - +
654A TRP* 2.9 28.8 + - + +
675A LEU* 3.7 4.7 - - - -
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Residues in contact with GLY 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A VAL* 3.6 2.6 - - - -
631A ASN* 2.7 32.1 + - - -
632A CYS* 3.1 15.9 + - - +
644A THR* 1.3 74.2 - - - +
646A SER* 1.3 54.4 + - - -
650A THR 3.9 3.4 - - - -
651A VAL* 4.5 0.7 - - - -
672A ILE* 3.7 29.6 - - - -
675A LEU* 3.5 8.2 - - - +
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Residues in contact with SER 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A HIS* 3.0 35.6 + - - -
628A ALA 3.3 9.5 + - - -
629A ASP 2.7 20.2 + - - -
630A VAL* 4.6 0.4 - - - -
631A ASN* 4.1 2.9 - - - +
645A GLY* 1.3 72.9 - - - -
647A ALA* 1.3 62.7 + - - +
648A ASP* 3.0 25.2 + - - -
649A ARG 3.0 15.8 + - - -
650A THR 3.3 6.7 + - - -
672A ILE* 3.3 20.4 + - - +
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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