Contacts of the helix formed by residues 702 - 710 (chain A) in PDB entry 1SC7
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 GLU 702 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A ILE* 4.4 21.1 - - + +
655A LYS* 5.5 6.7 - - - +
698A LEU* 2.9 21.6 + - + +
699A MET* 4.9 3.4 - - - -
701A LEU* 1.3 75.3 - - - +
703A VAL* 1.3 61.9 + - + +
705A ALA* 3.5 8.8 - - + +
706A THR* 3.0 35.7 + - - -
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Residues in contact with VAL 703 (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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613A PRO* 3.3 30.1 - - + +
614A ALA* 4.4 15.3 - - + -
617A LEU* 3.8 27.2 - - + +
699A MET* 3.5 25.0 - - + +
700A LYS 3.4 6.2 + - - +
701A LEU 3.2 0.4 - - - -
702A GLU* 1.3 77.8 - - + +
704A GLN* 1.3 59.8 + - + +
705A ALA 3.1 5.2 - - - -
706A THR* 3.5 4.2 + - - -
707A ASP* 3.2 26.8 + - + +
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Residues in contact with GLN 704 (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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613A PRO* 6.5 0.7 - - + -
647A LEU* 5.2 9.9 - - + +
700A LYS* 3.0 41.0 + - + +
701A LEU* 3.9 15.7 - - + +
702A GLU 3.4 0.2 - - - -
703A VAL* 1.3 78.9 - - + +
705A ALA* 1.3 57.0 + - - +
707A ASP* 3.9 11.0 - - + +
708A ARG* 3.4 24.9 + - - +
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Residues in contact with ALA 705 (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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644A MET* 3.9 24.4 - - + +
647A LEU* 5.0 4.7 - - + -
651A ILE* 3.8 20.4 - - + -
701A LEU 3.3 11.9 + - - +
702A GLU* 3.5 13.5 - - + +
703A VAL 3.1 0.4 - - - -
704A GLN* 1.3 76.2 - - - +
706A THR* 1.3 59.6 + - - +
707A ASP 3.2 1.8 - - - -
708A ARG* 3.5 1.8 + - - -
709A GLU* 3.1 29.9 + - - +
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Residues in contact with THR 706 (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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617A LEU* 4.4 6.5 - - + -
621A ARG* 3.7 18.6 - - - +
702A GLU* 3.0 26.2 + - - -
703A VAL* 3.5 6.3 + - - -
705A ALA* 1.3 75.5 - - - +
707A ASP* 1.3 62.2 + - - +
709A GLU* 3.7 5.4 + - - +
710A GLU* 3.3 46.5 + - + +
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Residues in contact with ASP 707 (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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616A ILE* 4.3 2.6 - - - +
617A LEU* 3.9 23.0 + - + +
620A ASN* 3.4 42.3 + - - +
624A ARG* 3.6 9.3 + - - +
703A VAL* 3.2 18.6 + - + +
704A GLN* 3.9 11.9 - - - +
706A THR* 1.3 77.3 - - - +
708A ARG* 1.3 64.2 + - - +
710A GLU* 3.6 6.5 + - - -
711A ASN* 3.3 24.1 + - - +
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Residues in contact with ARG 708 (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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635A ALA* 5.0 11.3 - - - +
640A PHE* 3.4 34.6 - - + -
644A MET* 4.4 9.9 - - - -
647A LEU* 4.9 11.9 - - + -
704A GLN 3.4 17.4 + - - +
705A ALA* 3.5 3.3 + - - +
706A THR 3.5 0.2 - - - -
707A ASP* 1.3 79.9 + - - +
709A GLU* 1.3 63.6 + - - +
711A ASN* 3.4 34.8 + - - +
716A LEU* 6.1 1.4 - - - +
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Residues in contact with GLU 709 (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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640A PHE* 3.7 19.4 - - - -
644A MET* 4.0 23.8 - - + +
705A ALA 3.1 19.8 + - - +
706A THR* 4.1 6.1 - - - +
707A ASP 3.4 0.4 - - - -
708A ARG* 1.3 76.0 - - - +
710A GLU* 1.3 63.1 + - + +
711A ASN 3.4 0.4 + - - -
712A LYS* 4.0 30.1 + - - +
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Residues in contact with GLU 710 (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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617A LEU* 4.7 1.4 - - - +
621A ARG* 3.0 31.5 + - - -
624A ARG* 3.0 51.3 + - - +
706A THR* 3.3 33.9 + - + +
707A ASP 3.6 0.6 + - - +
708A ARG 3.3 0.4 - - - -
709A GLU* 1.3 78.0 - - + +
711A ASN* 1.3 55.8 + - - +
712A LYS* 3.3 8.3 + - - -
714A ILE* 3.7 10.7 - - - +
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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