Contacts of the strand formed by residues 637 - 644 (chain A) in PDB entry 2XT6
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 637 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A GLU* 3.3 18.6 - - + +
534A VAL* 3.7 29.2 - - + -
617A VAL* 3.5 15.3 - - + +
620A LYS* 4.0 26.7 - - + -
621A GLN* 2.9 38.0 + - + +
624A LEU* 3.4 32.8 - - + -
635A PHE 3.1 1.4 - - - -
636A SER* 1.4 78.1 - - - +
638A VAL* 1.3 62.1 + - - +
728A ARG* 3.3 6.6 + - - -
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Residues in contact with VAL 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A VAL* 5.7 1.1 - - + -
525A CYS* 3.8 24.0 - - + -
530A LEU* 3.6 32.3 - - + -
532A GLU 2.8 15.6 + - - +
533A VAL* 3.4 11.0 - - + +
534A VAL 3.0 26.6 + - - +
617A VAL* 4.5 2.9 - - - -
635A PHE 4.4 0.2 - - - +
637A VAL* 1.3 75.9 - - - +
639A PRO* 1.4 79.1 - - + +
640A LEU* 3.5 1.4 + - + -
670A GLY 4.7 0.2 - - - +
672A ILE* 4.3 14.6 - - + -
728A ARG* 3.8 22.7 - - - +
729A GLN* 4.9 0.4 - - - +
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Residues in contact with PRO 639 (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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534A VAL 3.5 6.1 - - - +
613A LEU* 3.8 15.7 - - + -
614A GLU* 3.7 6.7 - - - +
617A VAL* 3.8 22.9 - - + -
637A VAL 3.9 3.4 - - - +
638A VAL* 1.4 88.1 - - + +
640A LEU* 1.3 57.9 + - - +
641A MET 4.0 1.1 - - - -
668A THR* 3.5 17.3 - - - +
670A GLY 3.3 18.4 - - - +
671A THR* 3.4 24.7 - - + +
672A ILE* 3.0 25.1 + - - -
728A ARG* 3.9 6.1 - - - +
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Residues in contact with LEU 640 (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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518A MET* 4.2 17.3 - - + -
521A VAL* 4.0 21.3 - - + -
522A ILE* 4.2 8.3 - - + -
533A VAL* 3.8 20.9 - - + -
534A VAL 2.9 7.3 + - - +
535A ILE* 3.2 32.1 - - + +
536A ALA 3.1 24.4 + - - +
613A LEU* 4.0 1.0 - - - +
638A VAL* 3.5 1.1 + - + -
639A PRO* 1.3 71.7 - - - +
641A MET* 1.3 59.0 + - - +
642A LEU* 4.4 8.1 - - + -
672A ILE* 3.5 25.4 - - + +
674A ILE* 3.8 28.0 - - + -
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Residues in contact with MET 641 (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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536A ALA* 3.5 10.3 - - + +
610A ASP* 3.4 45.1 - - + +
613A LEU* 3.8 17.9 - - + -
614A GLU* 3.1 29.4 - - + +
639A PRO 4.0 0.2 - - - -
640A LEU* 1.3 73.6 - - - +
642A LEU* 1.4 63.8 + - - +
643A HIS* 3.3 36.4 + - + +
657A THR* 4.3 5.4 - - + -
671A THR* 3.9 9.4 - - + -
672A ILE 2.9 8.7 + - - -
673A HIS* 3.3 16.2 - - + +
674A ILE 3.0 22.0 + - - -
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Residues in contact with LEU 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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514A VAL* 4.0 16.4 - - + -
518A MET* 3.7 31.6 - - + -
535A ILE* 5.0 1.1 - - + -
536A ALA 2.8 11.7 + - - +
537A MET* 3.7 39.1 - - + -
538A PRO* 3.7 15.8 - - + +
540A ARG 5.6 1.8 - - - +
545A VAL* 5.3 0.2 - - + -
607A GLU* 4.7 1.6 - - - +
610A ASP* 4.9 2.1 - - - +
640A LEU* 4.4 11.9 - - + +
641A MET* 1.4 75.4 - - - +
643A HIS* 1.3 73.6 + - - +
674A ILE* 3.3 39.3 - - + +
676A VAL* 4.3 11.2 - - + -
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Residues in contact with HIS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PRO* 4.3 10.5 - - - -
607A GLU* 2.5 39.4 + - - +
610A ASP* 3.7 3.8 + - - -
641A MET* 3.3 46.8 + - + -
642A LEU* 1.3 73.8 + - - +
644A GLY* 1.3 62.5 + - - +
648A PHE* 3.2 36.5 - + + -
654A VAL* 5.1 1.1 - - + -
673A HIS* 2.8 30.6 + + + -
674A ILE 3.0 10.9 + - - +
675A VAL* 3.5 6.9 - - + -
676A VAL* 2.9 31.7 + - - +
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Residues in contact with GLY 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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538A PRO* 4.5 7.1 - - - +
606A LEU* 6.3 0.4 - - - +
607A GLU* 4.0 4.8 + - - -
643A HIS* 1.3 73.6 - - - +
645A ASP* 1.3 65.1 + - - -
646A ALA 3.5 2.2 - - - -
647A ALA* 3.7 7.1 + - - +
648A PHE* 3.1 25.5 + - - +
675A VAL* 3.7 3.4 - - - -
676A VAL* 3.7 9.9 - - - -
678A ASN* 6.0 0.2 - - - -
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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
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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