Contacts of the strand formed by residues 630 - 635 (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 VAL 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A TRP* 3.4 8.7 - - - -
603A GLY* 3.4 9.5 - - - +
604A GLY 3.1 23.2 + - - +
607A ARG* 3.8 23.1 - - - +
608A VAL* 3.9 16.4 - - - +
609A ALA* 4.2 3.6 - - + +
623A PHE 5.4 0.4 - - - +
626A HIS* 3.7 29.2 - - + -
628A ALA 3.4 0.2 + - - -
629A ASP* 1.3 71.0 - - - +
631A ASN* 1.3 63.0 + - - +
632A CYS 3.7 7.4 - - - +
633A THR* 3.7 29.8 - - + -
644A THR* 4.2 11.2 - - + -
645A GLY 3.7 3.1 - - - +
646A SER* 4.3 0.2 - - - +
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Residues in contact with ASN 631 (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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589A TRP* 3.6 22.5 + - + +
590A ASP* 3.4 18.5 - - - +
629A ASP* 3.5 20.6 - - - +
630A VAL* 1.3 74.6 - - - +
632A CYS* 1.3 61.9 + - - +
645A GLY 2.7 11.8 + - - +
647A ALA* 3.8 16.7 - - - +
671A PRO* 3.8 21.4 - - - +
672A ILE 3.0 29.1 + - - +
673A HIS* 4.3 14.1 + - + -
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Residues in contact with CYS 632 (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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590A ASP* 3.5 9.6 - - - +
630A VAL* 3.7 2.1 - - - +
631A ASN* 1.3 84.8 - - - +
633A THR* 1.3 71.9 + - - +
634A ARG* 5.2 2.9 - - - +
643A ALA 4.4 0.2 - - - -
644A THR* 3.2 4.3 - - - -
645A GLY 3.1 28.3 + - - +
672A ILE* 3.8 12.6 - - - -
673A HIS* 3.5 40.6 - - - -
674A SER* 3.8 6.1 - - - -
675A LEU* 4.1 19.5 - - + +
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Residues in contact with THR 633 (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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590A ASP* 3.0 25.6 + - + +
591A THR* 4.1 0.9 + - - -
592A GLN* 3.6 9.5 - - - +
601A VAL* 3.7 28.2 + - - +
602A SER* 3.9 1.7 - - - -
603A GLY* 3.8 17.0 - - - +
609A ALA* 3.9 14.8 - - + -
630A VAL* 3.7 20.4 - - + -
632A CYS* 1.3 81.3 - - - +
634A ARG* 1.3 81.0 + - - +
642A VAL* 5.0 0.2 - - - -
643A ALA 3.4 6.5 - - - -
644A THR* 4.1 4.3 - - + -
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Residues in contact with ARG 634 (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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590A ASP* 2.8 28.9 + - - -
591A THR 4.8 0.8 + - - -
592A GLN* 3.4 31.6 - - - +
601A VAL* 4.6 0.8 - - - +
632A CYS* 4.4 3.0 - - - +
633A THR* 1.3 101.8 + - - +
635A PHE* 1.3 63.9 + - - +
642A VAL* 3.4 6.0 - - - +
643A ALA 2.8 33.4 + - - -
675A LEU* 3.5 49.9 + - + +
676A THR* 4.9 2.9 - - - +
677A PHE* 3.7 12.3 - - + -
718A ARG* 4.9 18.5 - - - +
782A HIS* 6.4 0.4 - - - -
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Residues in contact with PHE 635 (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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592A GLN* 2.7 45.2 + - - +
593A PHE 3.5 9.4 - - - -
594A SER* 3.5 25.4 - - - -
595A PRO* 3.5 18.5 - - + +
599A TYR* 4.2 3.8 - + + -
600A PHE* 3.8 9.2 - - - -
601A VAL* 3.7 15.9 - - + -
611A LEU* 3.5 32.8 - - + -
634A ARG* 1.3 74.4 - - - +
636A HIS* 1.3 62.9 + - - +
637A PRO* 3.8 1.4 - - - +
639A SER* 3.9 30.5 - - - -
641A TYR 3.7 7.2 - - - -
642A VAL* 3.6 16.6 - - + -
656A VAL* 4.5 0.4 - - + -
677A PHE* 3.2 15.7 - - - +
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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