Contacts of the helix formed by residues 621 - 628 (chain A) in PDB entry 2C11
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A PRO* 3.7 27.8 - - + -
218A LEU* 5.3 0.9 - - - +
381A THR* 5.4 1.6 - - - +
383A ARG* 3.7 35.9 - - - -
615A LEU* 3.9 7.9 - - + -
619A SER* 3.7 13.0 - - - +
620A SER* 1.3 80.0 + - - +
622A ALA* 1.3 69.0 + - - +
623A ARG 3.2 2.9 - - - -
624A GLY* 2.8 18.0 + - - -
625A PHE* 4.1 10.1 - - + -
653A PRO* 3.1 28.2 - - + +
654A TRP* 3.7 23.1 - - + +
1739A CL 4.0 15.7 - - + -
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Residues in contact with ALA 622 (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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615A LEU* 4.1 7.1 - - + +
616A PRO 3.2 26.7 - - - +
617A GLN* 4.1 13.2 - - + +
619A SER 3.2 14.2 + - - +
620A SER 3.6 0.2 - - - -
621A MET* 1.3 78.7 - - - +
623A ARG* 1.3 64.7 + - + +
624A GLY 3.1 0.9 + - - -
625A PHE* 3.2 28.8 + - - -
626A SER* 3.4 10.7 + - - -
629A ARG* 6.3 1.1 - - - +
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Residues in contact with ARG 623 (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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619A SER 5.1 0.2 + - - -
620A SER 4.9 3.5 + - - +
621A MET 2.9 4.6 + - - +
622A ALA* 1.3 75.2 - - + +
624A GLY* 1.3 61.7 + - - +
625A PHE 3.0 2.2 + - - -
626A SER* 3.4 13.5 + - - -
629A ARG* 5.7 3.0 - - - +
653A PRO 4.7 1.1 - - - +
656A PRO* 3.3 24.9 - - + +
658A VAL 4.9 0.3 - - - +
659A ASP* 2.6 57.5 + - - +
660A PHE 4.8 0.2 + - - -
661A SER* 3.5 23.5 + - - -
662A ASP* 3.3 13.3 + - - -
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Residues in contact with GLY 624 (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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385A VAL* 4.8 1.8 - - - +
621A MET 2.8 18.6 + - - -
623A ARG* 1.3 70.9 - - - +
625A PHE* 1.3 70.4 + - - +
627A TRP* 5.2 0.2 - - - -
644A SER 5.5 0.5 - - - +
645A SER* 3.8 9.9 + - - -
649A ASN* 3.2 24.4 + - - +
653A PRO* 3.7 11.4 - - - -
656A PRO* 3.2 21.9 - - - +
658A VAL 5.0 1.4 - - - +
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Residues in contact with PHE 625 (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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369A LEU* 4.0 28.0 - - + -
371A ILE* 3.9 17.5 - - + -
383A ARG* 4.4 9.4 - - + -
385A VAL* 3.4 32.8 - - + -
615A LEU* 3.8 33.9 - - + -
621A MET* 4.1 23.8 - - - -
622A ALA* 3.2 13.8 + - - +
623A ARG 3.0 0.4 - - - -
624A GLY* 1.3 82.0 - - - +
626A SER* 1.3 59.3 + - - +
627A TRP* 3.1 25.4 - - + +
628A GLU* 3.0 26.3 + - - +
629A ARG 4.4 0.3 + - - -
653A PRO* 4.4 13.2 - - + -
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Residues in contact with SER 626 (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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622A ALA 3.4 6.9 + - - -
623A ARG* 3.4 16.1 + - - -
625A PHE* 1.3 73.2 - - - +
627A TRP* 1.3 63.3 + - - +
628A GLU 3.1 0.2 - - - -
629A ARG* 3.0 29.3 + - - +
630A TYR* 4.1 7.8 - - - -
659A ASP* 3.2 5.7 + - - -
660A PHE* 3.0 36.4 + - - +
661A SER* 3.1 29.7 + - - -
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Residues in contact with TRP 627 (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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367A GLU* 3.6 35.7 - - + +
368A ALA 4.5 0.4 - - - -
369A LEU* 4.0 21.1 - - + -
523A SER* 3.8 35.0 - - - -
524A ALA* 3.8 9.0 - - - -
525A HIS* 3.3 54.1 - + + +
625A PHE* 3.8 22.2 - - + +
626A SER* 1.3 75.6 + - - +
628A GLU* 1.3 83.2 + - - +
629A ARG 2.9 7.4 + - - -
630A TYR* 3.0 16.2 + - - +
644A SER* 3.9 20.9 - - - -
645A SER* 4.0 3.5 + - - -
660A PHE* 3.3 30.3 - - + -
679A THR* 3.4 21.8 + - + -
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Residues in contact with GLU 628 (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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369A LEU* 3.6 28.1 - - + +
371A ILE* 3.7 15.9 - - - +
521A THR* 4.1 10.6 + - - -
523A SER* 3.7 23.6 + - - +
579A VAL* 3.6 11.3 - - - +
611A ALA* 5.9 0.2 - - - +
612A GLY 5.0 3.8 - - - +
613A GLU 4.6 0.9 - - - +
614A PRO* 3.2 28.1 - - + +
615A LEU* 3.1 21.6 + - - +
625A PHE* 3.0 19.4 + - - +
627A TRP* 1.3 92.8 - - + +
629A ARG* 1.3 55.7 + - - +
630A TYR 3.1 5.3 + - - +
679A THR* 4.6 4.5 - - + +
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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