Contacts of the helix formed by residues 621 - 628 (chain B) in PDB entry 2C10
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 MET 621 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PRO* 3.8 28.5 - - + -
217B GLY 5.3 1.6 - - - +
381B THR* 5.2 2.7 - - - +
383B ARG* 3.8 38.6 - - - -
615B LEU* 3.9 8.3 - - + -
619B SER* 3.1 14.0 - - - +
620B SER* 1.3 79.0 + - - +
622B ALA* 1.3 63.9 + - - +
623B ARG 3.3 3.1 - - - -
624B GLY* 3.0 16.9 + - - -
625B PHE* 3.8 11.1 - - + -
653B PRO* 3.7 26.1 - - + +
654B TRP* 3.8 22.9 - - + +
1778B CL 4.1 12.3 - - + -
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Residues in contact with ALA 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B LEU* 4.4 18.6 - - + +
616B PRO 3.9 18.6 - - - +
617B GLN* 4.2 13.5 - - + +
619B SER* 3.4 18.6 + - - +
620B SER 3.5 0.2 - - - -
621B MET* 1.3 79.3 - - - +
623B ARG* 1.3 60.3 - - + +
624B GLY 3.0 0.2 - - - -
625B PHE* 3.0 26.9 + - - +
626B SER* 3.3 12.6 + - - -
629B ARG* 6.1 3.8 - - + -
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Residues in contact with ARG 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617B GLN* 5.6 13.2 - - - +
619B SER 5.5 2.0 - - - +
620B SER 5.0 7.0 - - - +
621B MET 3.2 0.8 + - - -
622B ALA* 1.3 80.5 - - + +
624B GLY* 1.3 60.3 + - - +
625B PHE 3.1 2.4 + - - -
626B SER* 3.9 12.0 + - - -
629B ARG* 5.8 0.8 - - - +
653B PRO 4.8 1.8 - - - +
654B TRP 6.0 0.4 - - - +
656B PRO* 3.6 27.4 - - + +
659B ASP* 3.3 34.6 + - - +
661B SER* 3.2 34.5 + - - -
662B ASP* 4.9 6.3 + - - -
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Residues in contact with GLY 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B VAL* 4.7 3.6 - - - +
621B MET 3.0 11.3 + - - -
622B ALA 3.0 2.4 + - - -
623B ARG* 1.3 78.5 - - - +
625B PHE* 1.3 68.3 + - - +
627B TRP* 5.1 0.2 + - - -
645B SER* 5.0 1.6 + - - -
649B ASN* 2.9 34.6 + - - +
653B PRO* 3.6 23.4 + - - -
656B PRO* 3.9 4.0 - - - -
658B VAL 5.1 0.2 - - - -
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Residues in contact with PHE 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LEU* 3.7 31.6 - - + -
371B ILE* 4.1 9.4 - - + -
383B ARG* 4.3 10.8 - - + -
385B VAL* 3.6 29.8 - - + -
615B LEU* 3.8 32.3 - - + -
621B MET* 3.8 29.4 - - + -
622B ALA* 3.0 10.8 + - - +
624B GLY* 1.3 85.2 - - - +
626B SER* 1.3 56.7 + - - +
627B TRP* 3.1 33.0 - - + +
628B GLU* 3.1 27.9 + - - +
653B PRO* 4.5 6.7 - - + -
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Residues in contact with SER 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B ALA 3.3 11.2 + - - -
623B ARG* 3.9 11.5 + - - -
625B PHE* 1.3 72.0 - - - +
627B TRP* 1.3 61.2 + - - +
628B GLU 3.0 6.9 + - - -
629B ARG* 3.2 32.2 + - - +
630B TYR* 3.6 10.8 - - - -
659B ASP* 2.7 25.8 + - - -
660B PHE* 3.5 5.2 + - - +
661B SER* 3.1 28.5 + - - -
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Residues in contact with TRP 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B GLU* 3.7 37.8 - - + +
369B LEU* 3.8 33.2 - - + -
523B SER* 3.8 21.1 - - - -
524B ALA* 3.7 15.0 - - - -
525B HIS* 3.4 43.2 - + + +
624B GLY 5.4 0.2 - - - -
625B PHE* 3.7 25.0 - - + +
626B SER* 1.3 78.7 + - - +
628B GLU* 1.3 66.3 + - - +
630B TYR* 3.3 11.3 + - - +
644B SER* 4.1 20.4 - - - -
645B SER* 4.7 3.2 + - - -
660B PHE* 3.6 22.2 - - + +
679B THR* 3.0 45.7 + - + -
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Residues in contact with GLU 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LEU* 3.4 25.5 - - + +
371B ILE* 3.4 21.7 - - - +
521B THR* 4.2 6.6 + - - -
523B SER* 3.8 20.9 + - - +
579B VAL* 3.3 15.8 - - - +
612B GLY 5.1 3.8 - - - +
613B GLU 4.3 2.6 - - - +
614B PRO* 3.6 24.2 - - + +
615B LEU* 3.2 21.5 + - - +
625B PHE* 3.1 19.5 + - - +
626B SER 3.0 0.6 - - - -
627B TRP* 1.3 88.0 - - + +
629B ARG* 1.3 63.7 + - + +
630B TYR 3.2 1.3 - - - +
679B THR* 4.4 5.0 - - + +
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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