Contacts of the strand formed by residues 651 - 656 (chain C) in PDB entry 7REQ
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 651 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C ARG 3.8 4.9 - - - +
600C ILE* 3.3 30.2 - - + +
601C LEU 3.1 23.0 + - - -
626C PHE* 6.0 0.9 - - + -
649C VAL* 3.5 6.6 - - - +
650C HIS* 1.3 83.9 - - + +
652C VAL* 1.3 75.1 + - - +
653C GLY 4.2 0.7 - - - +
680C ILE* 4.1 0.7 - - - -
681C LEU* 3.2 20.2 - - + +
683C THR* 4.1 25.8 - - + +
718C LEU* 4.1 15.9 - - + -
722C LEU* 4.4 15.5 - - + -
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Residues in contact with VAL 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C LEU* 3.5 14.8 - - + +
603C ALA* 4.0 9.6 - - + -
640C THR* 3.9 17.0 - - + -
644C ALA* 3.6 29.8 - - + -
649C VAL* 4.5 0.7 - - + -
651C VAL* 1.3 73.9 - - - +
653C GLY* 1.3 60.7 + - - +
654C VAL* 3.5 3.5 + - + -
668C LEU* 3.7 28.7 - - + -
672C LEU* 4.1 12.6 - - + -
680C ILE* 3.9 13.0 - - + -
681C LEU 2.9 8.4 + - - +
682C ILE* 3.4 4.5 - - + +
683C THR 3.0 25.8 + - - +
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Residues in contact with GLY 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C ILE* 3.9 8.0 - - - +
601C LEU 2.8 12.1 + - - -
602C LEU* 3.4 9.2 - - - +
603C ALA 2.9 22.6 + - - -
651C VAL 3.9 2.6 + - - -
652C VAL* 1.3 70.7 - - - +
654C VAL* 1.3 62.5 + - - -
655C SER* 3.6 1.4 + - - -
683C THR* 3.2 19.1 - - - -
2800C B12 3.9 17.0 - - - +
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Residues in contact with VAL 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603C ALA* 3.7 9.2 - - + +
605C MET* 3.5 35.7 - - + +
652C VAL* 4.2 6.5 - - + -
653C GLY* 1.3 72.4 - - - -
655C SER* 1.3 57.5 + - - +
656C SER* 4.2 20.6 - - - -
665C VAL* 4.4 7.9 - - + -
668C LEU* 3.8 19.7 - - + -
682C ILE* 4.2 8.7 - - + -
683C THR 2.9 17.5 + - - +
684C VAL* 4.3 10.5 - - + -
685C GLY* 2.7 32.9 + - - -
2800C B12 4.1 2.4 - - - -
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Residues in contact with SER 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LEU* 6.3 0.9 - - - -
603C ALA 3.1 14.4 + - - +
604C LYS* 2.8 32.8 + - - -
605C MET 5.1 1.6 + - - -
608C ASP* 3.9 0.3 - - - +
613C GLY 4.4 0.5 - - - -
614C GLN* 3.8 29.5 + - - -
653C GLY 3.6 1.9 + - - -
654C VAL* 1.3 73.7 - - - +
656C SER* 1.3 58.2 + - - +
657C LEU* 3.8 13.0 - - - +
685C GLY 3.5 3.8 - - - -
2800C B12 2.9 31.2 + - - -
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Residues in contact with SER 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608C ASP* 3.6 4.1 + - - -
654C VAL* 4.2 15.0 - - - -
655C SER* 1.3 74.0 + - - +
657C LEU* 1.3 61.9 + - - +
658C ALA 4.4 2.3 + - - -
659C GLY 4.5 0.4 + - - -
660C GLY 4.3 6.2 + - - -
661C HIS* 3.8 37.3 + - - +
664C LEU* 5.3 5.6 - - - +
684C VAL* 4.8 2.9 - - - -
685C GLY 2.7 14.4 + - - +
686C GLY* 3.4 2.9 - - - -
687C VAL 3.2 23.7 + - - +
688C ILE* 4.9 2.2 - - - +
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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