Contacts of the helix formed by residues 621 - 628 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PRO* 3.8 26.9 - - + -
217C GLY 5.3 2.0 - - - +
218C LEU* 6.2 0.2 - - - -
381C THR* 5.4 2.7 - - - +
383C ARG* 3.6 36.3 - - - -
615C LEU* 3.8 9.4 - - + -
619C SER* 3.0 14.7 + - - +
620C SER* 1.3 79.4 + - - +
622C ALA* 1.3 65.6 + - - +
623C ARG 3.1 3.1 - - - -
624C GLY* 2.8 19.5 + - - -
625C PHE* 4.0 10.8 - - + -
653C PRO* 3.6 19.3 - - + +
654C TRP* 3.7 26.9 - - + +
1774C CL 4.2 14.1 - - + -
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Residues in contact with ALA 622 (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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615C LEU* 4.3 12.1 - - + +
616C PRO 3.6 20.2 - - - +
617C GLN* 4.2 14.6 - - + +
619C SER* 3.3 17.9 + - - +
621C MET* 1.3 79.5 - - - +
623C ARG* 1.3 64.7 + - + +
624C GLY 3.1 1.2 + - - -
625C PHE* 3.1 28.8 + - + -
626C SER* 3.5 11.3 + - - -
629C ARG* 6.3 1.3 - - + -
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Residues in contact with ARG 623 (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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617C GLN* 3.4 33.8 + - - +
619C SER 5.5 2.5 - - - +
620C SER 5.3 6.1 - - - +
621C MET 2.9 2.1 + - - +
622C ALA* 1.3 77.7 - - + +
624C GLY* 1.3 57.4 + - - +
625C PHE 3.1 2.6 + - - -
626C SER* 3.8 14.7 + - - -
629C ARG* 5.0 4.3 - - - +
653C PRO 4.7 1.8 - - - +
654C TRP 5.7 0.7 - - - +
656C PRO* 3.6 24.1 - - + +
658C VAL 4.2 0.2 - - - +
659C ASP* 3.2 37.1 + - - +
661C SER* 3.9 19.4 + - - -
662C ASP* 5.2 4.6 + - - -
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Residues in contact with GLY 624 (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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385C VAL* 4.8 4.3 - - - +
621C MET 2.8 19.5 + - - -
623C ARG* 1.3 71.8 - - - +
625C PHE* 1.3 67.7 + - - +
645C SER* 4.9 2.3 + - - -
649C ASN* 3.1 35.2 + - - +
653C PRO* 3.4 23.7 + - - -
656C PRO* 4.2 2.5 - - - -
658C VAL 4.9 0.7 - - - -
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Residues in contact with PHE 625 (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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369C LEU* 3.7 31.6 - - + -
371C ILE* 4.1 10.1 - - + -
383C ARG* 4.6 6.3 - - + -
385C VAL* 3.8 19.1 - - + -
615C LEU* 3.8 29.4 - - + -
621C MET* 4.0 28.7 - - + -
622C ALA* 3.1 10.7 + - - -
623C ARG 3.1 0.4 - - - -
624C GLY* 1.3 84.5 - - - +
626C SER* 1.3 56.3 + - - +
627C TRP* 3.1 37.2 - - + +
628C GLU* 3.0 38.2 + - - +
653C PRO* 4.6 7.6 - - + -
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Residues in contact with SER 626 (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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622C ALA 3.8 10.8 - - - -
623C ARG* 3.8 12.2 + - - -
625C PHE* 1.3 71.0 - - - +
627C TRP* 1.3 62.1 + - - +
628C GLU 3.0 5.2 - - - -
629C ARG* 3.0 36.2 + - - +
630C TYR* 3.6 8.7 - - - -
659C ASP* 2.7 28.4 + - - -
660C PHE* 3.4 7.1 + - - +
661C SER* 3.3 22.0 + - - -
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Residues in contact with TRP 627 (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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367C GLU* 3.6 42.4 - - + +
369C LEU* 3.6 31.9 - - + -
523C SER* 3.8 28.9 - - - -
524C ALA 3.9 6.7 - - - -
525C HIS* 3.4 50.3 - + + +
625C PHE* 3.6 30.0 - - + +
626C SER* 1.3 79.2 + - - +
628C GLU* 1.3 83.0 + - - +
629C ARG 3.0 1.4 + - - -
630C TYR* 3.1 11.3 + - - +
644C SER* 3.8 22.5 + - - -
645C SER* 4.5 2.8 + - - -
660C PHE* 3.6 20.8 - - + +
679C THR* 3.0 26.8 + - + -
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Residues in contact with GLU 628 (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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369C LEU* 3.6 24.4 - - + +
371C ILE* 3.5 15.2 - - - +
521C THR* 4.4 8.0 + - - -
523C SER* 4.1 16.2 + - - +
579C VAL* 3.4 15.6 - - - +
612C GLY 5.1 3.1 - - - +
613C GLU 4.1 3.5 - - - +
614C PRO* 3.3 28.5 - - + +
615C LEU* 3.0 18.6 + - - +
625C PHE* 3.0 32.0 + - - +
626C SER* 4.7 0.4 - - - -
627C TRP* 1.3 90.0 - - + +
629C ARG* 1.3 60.6 + - + +
630C TYR 3.4 2.3 + - - +
679C THR* 4.4 5.3 - - - +
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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