Contacts of the helix formed by residues 619 - 631 (chain B) in PDB entry 2C7A
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 CYS 619 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A ASN* 4.5 5.6 - - + +
602B LEU 5.2 0.2 - - - -
603B CYS* 3.8 18.8 - - - -
604B ALA 4.7 2.2 - - - -
609B CYS* 3.9 14.1 - - + -
611B VAL* 5.3 1.6 - - + +
615B ARG 4.4 0.4 + - - -
616B ARG 4.1 4.7 + - - +
618B ASN* 1.3 81.4 - - + +
620B PRO* 1.3 62.7 - - - +
621B ALA* 3.2 4.0 - - - -
622B CYS* 3.6 15.8 - - + +
623B ARG* 3.0 28.4 + - - +
1640B ZN 2.3 37.2 - - - -
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Residues in contact with PRO 620 (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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617A LYS* 5.8 2.0 - - - +
618A ASN* 4.1 15.5 - - - +
590B PHE* 3.5 19.6 - - + -
601B TYR* 3.6 48.2 - - + -
616B ARG 5.3 0.4 - - - +
617B LYS 4.0 8.9 - - - +
618B ASN 3.5 10.3 - - - +
619B CYS* 1.3 84.0 - - - +
621B ALA* 1.3 60.1 + - - +
623B ARG* 4.2 2.0 - - + -
624B LEU* 2.8 34.1 + - - +
12C T 5.1 9.2 - - - +
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Residues in contact with ALA 621 (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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601B TYR* 3.5 30.3 - - + +
602B LEU 3.8 1.3 - - - -
603B CYS* 3.4 35.4 - - + +
619B CYS* 3.2 1.7 - - - -
620B PRO* 1.3 79.8 - - - +
622B CYS* 1.3 57.6 + - - +
624B LEU* 3.7 5.4 - - - +
625B ARG* 2.9 44.6 + - - +
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Residues in contact with CYS 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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603B CYS* 3.8 1.6 - - - -
607B ASN* 3.5 25.4 - - - -
609B CYS* 3.5 30.1 - - + +
611B VAL* 4.0 11.3 - - + +
619B CYS* 3.4 8.2 + - + +
620B PRO 3.3 0.4 - - - -
621B ALA* 1.3 74.9 - - - +
623B ARG* 1.3 60.2 + - - +
625B ARG* 3.7 9.4 - - - +
626B LYS* 3.0 30.1 + - - +
1640B ZN 2.3 35.2 - - - -
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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
----------------------------------------------------------
569B ILE* 4.0 6.7 - - + +
586B SER* 3.2 21.4 + - - -
587B CYS* 3.3 32.7 - - - +
590B PHE* 3.4 44.7 - - + +
611B VAL* 3.8 27.7 - - + +
616B ARG* 3.6 39.4 + - - +
617B LYS* 4.3 5.8 - - - +
619B CYS 3.0 17.7 + - - +
620B PRO* 3.8 3.4 - - + +
622B CYS* 1.3 74.9 - - - +
624B LEU* 1.3 58.9 + - - +
626B LYS* 3.5 4.0 + - - +
627B CYS* 3.0 31.5 + - - -
12C T 4.7 2.4 - - - -
13C G 2.8 28.9 + - - -
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B PHE* 3.5 11.8 - - + -
591B PHE* 4.1 16.6 - - + -
594B ALA* 3.7 33.4 - - + +
595B MET* 3.8 26.9 - - - -
601B TYR* 4.3 15.5 - - + -
620B PRO 2.8 17.1 + - - +
621B ALA* 3.7 4.0 - - - +
623B ARG* 1.3 74.5 - - - +
625B ARG* 1.3 66.0 + - - +
627B CYS* 3.2 5.3 + - - +
628B CYS* 2.9 28.7 + - - -
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Residues in contact with ARG 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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601B TYR 5.5 3.4 + - - -
607B ASN* 3.8 30.3 + - - +
621B ALA* 2.9 44.0 + - - +
622B CYS* 3.7 8.8 - - - +
623B ARG 3.4 0.2 - - - -
624B LEU* 1.3 76.3 - - - +
626B LYS* 1.3 57.6 + - - +
628B CYS* 3.0 8.9 + - + +
629B GLN* 2.9 55.5 + - + +
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Residues in contact with LYS 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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568B LEU 3.5 17.3 + - - +
569B ILE* 2.6 37.5 + - + +
570B CYS 5.5 0.2 - - - -
611B VAL* 3.6 31.4 + - + +
622B CYS 3.0 17.0 + - - +
623B ARG* 3.6 6.3 - - - +
624B LEU 3.3 0.2 - - - -
625B ARG* 1.3 72.5 - - - +
627B CYS* 1.3 64.7 + - - +
629B GLN* 3.4 13.0 + - + +
630B ALA* 3.0 26.1 + - + +
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Residues in contact with CYS 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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569B ILE* 3.7 25.3 - - - +
587B CYS* 4.6 4.3 - - - -
590B PHE* 4.3 13.0 - - - -
591B PHE* 3.6 26.9 - - + -
623B ARG 3.0 24.8 + - - -
624B LEU* 3.2 8.5 + - - +
626B LYS* 1.3 73.3 - - - +
628B CYS* 1.3 64.2 + - - +
630B ALA* 3.2 8.3 + - - +
631B GLY 3.4 0.2 + - - -
632B MET* 3.1 49.7 + - - +
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Residues in contact with CYS 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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591B PHE* 4.1 17.7 - - - -
595B MET* 4.3 15.7 - - - -
624B LEU* 2.9 29.9 + - - +
625B ARG* 3.0 9.6 + - + +
627B CYS* 1.3 75.9 - - - +
629B GLN* 1.3 62.4 + - + +
631B GLY* 3.4 12.8 + - - -
632B MET 4.4 8.7 - - - +
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Residues in contact with GLN 629 (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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625B ARG* 2.9 40.2 + - + +
626B LYS* 3.9 13.8 + - - +
628B CYS* 1.3 73.6 - - + +
630B ALA* 1.3 64.5 + - - +
631B GLY* 3.1 3.2 + - - -
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Residues in contact with ALA 630 (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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568B LEU* 5.0 9.0 - - + +
569B ILE* 3.8 18.8 - - + -
581B VAL* 3.3 28.3 - - + +
626B LYS* 3.0 17.7 + - + +
627B CYS 3.2 5.8 + - - +
629B GLN* 1.3 76.5 - - - +
631B GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 631 (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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579B TYR 4.0 2.9 - - - +
580B GLY* 5.1 2.1 - - - -
581B VAL* 3.7 7.2 - - - +
627B CYS 3.4 1.0 + - - -
628B CYS 3.4 7.8 + - - -
629B GLN 3.1 4.9 - - - -
630B ALA* 1.3 80.2 - - - +
632B MET* 1.3 66.6 + - - +
633B VAL* 3.2 16.8 + - - +
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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