Contacts of the strand formed by residues 645 - 653 (chain A) in PDB entry 2V5I
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 THR 645 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A LEU* 3.5 7.3 - - - +
642A SER 2.9 14.5 + - - +
643A GLY 3.3 10.9 + - - -
644A SER* 1.3 76.9 + - - +
646A PRO* 1.3 77.9 - - + +
647A ASN 3.5 0.2 + - - -
648A ALA* 3.3 26.6 + - + +
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Residues in contact with PRO 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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616A LEU* 4.2 20.4 - - + -
617A ASP* 4.4 21.3 - - + +
641A LEU* 3.6 11.6 - - + -
644A SER 3.6 9.2 - - - +
645A THR* 1.3 95.1 - - + +
647A ASN* 1.3 79.0 + - - +
648A ALA 3.2 0.3 + - - -
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Residues in contact with ASN 647 (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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604A GLU* 5.6 0.6 + - - -
617A ASP* 5.4 0.9 + - - +
619A GLY* 4.9 3.0 - - - -
620A ALA* 3.8 14.0 + - - +
622A ARG* 3.7 28.0 - - - +
637A GLU* 5.3 2.5 - - - +
639A THR* 2.6 45.4 + - + +
640A ALA 3.8 8.0 + - - -
641A LEU* 4.6 0.4 - - - +
645A THR 3.5 0.2 + - - -
646A PRO* 1.3 83.6 + - - +
648A ALA* 1.3 63.2 + - - +
649A VAL 3.4 3.0 + - - -
650A SER* 4.4 10.2 - - - -
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Residues in contact with ALA 648 (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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640A ALA 3.2 4.0 + - - -
642A SER* 3.7 31.4 - - - +
645A THR* 3.3 26.9 - - + +
646A PRO 3.2 2.3 - - - -
647A ASN* 1.3 77.8 - - - +
649A VAL* 1.3 61.0 + - + +
650A SER* 4.2 1.6 + - - -
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Residues in contact with VAL 649 (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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638A LEU 4.1 0.3 - - - +
639A THR* 3.2 4.9 - - - -
640A ALA* 2.9 42.0 + - + +
641A LEU 5.5 0.2 - - - +
642A SER* 4.1 22.9 - - - -
647A ASN 4.4 0.2 - - - -
648A ALA* 1.3 80.6 - - + +
650A SER* 1.3 62.3 + - - +
664A PRO* 3.8 27.1 - - + -
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Residues in contact with SER 650 (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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637A GLU* 2.5 31.1 + - - +
638A LEU 3.5 5.2 - - - -
639A THR* 4.1 6.7 - - - +
647A ASN 4.4 8.1 - - - -
648A ALA 4.2 1.5 + - - -
649A VAL* 1.3 78.0 - - - +
651A LEU* 1.3 58.0 + - - +
652A LYS* 3.1 40.2 + - - +
662A GLU 4.0 1.9 - - - +
664A PRO* 3.4 16.9 - - - +
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Residues in contact with LEU 651 (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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636A THR 5.6 0.2 - - - +
637A GLU* 3.1 6.4 - - - +
638A LEU* 2.9 53.7 + - + +
650A SER* 1.3 71.2 - - - +
652A LYS* 1.3 61.4 + - - +
653A VAL* 4.1 13.9 - - + -
661A THR* 4.1 22.2 - - + -
662A GLU 3.4 11.0 - - - +
663A ILE* 4.6 11.4 - - + -
664A PRO* 3.9 17.8 - - + +
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Residues in contact with LYS 652 (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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635A TRP* 3.8 31.9 - - + -
636A THR 3.4 4.3 - - - -
637A GLU* 4.3 2.7 - - - -
650A SER* 3.1 48.1 + - - +
651A LEU* 1.3 73.4 - - - +
653A VAL* 1.3 62.3 + - - +
655A ARG* 4.1 11.7 - - + +
660A THR 3.7 1.4 - - - +
661A THR* 3.2 5.7 - - - +
662A GLU* 2.8 74.9 + - + +
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Residues in contact with VAL 653 (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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635A TRP* 3.2 3.6 - - - +
636A THR* 2.8 47.0 + - + +
651A LEU* 4.1 17.9 - - + -
652A LYS* 1.3 76.0 - - - +
654A ASN* 1.3 72.5 + - + +
655A ARG 3.4 1.6 - - - -
659A LYS 6.2 1.1 - - - -
660A THR 3.6 6.1 - - - +
661A THR* 4.4 13.2 - - + +
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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