Contacts of the strand formed by residues 700 - 705 (chain A) in PDB entry 1QFG
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 VAL 700 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A THR* 3.8 28.7 - - - +
253A VAL* 3.8 24.7 - - + +
663A VAL* 3.6 14.5 - - + +
664A GLY 4.7 0.2 - - - +
666A TYR* 3.4 14.7 - - - -
699A TYR* 1.3 73.6 - - - +
701A ALA* 1.3 63.7 + - - +
702A SER 3.6 20.4 - - - +
703A CYS* 3.9 6.5 - - - -
709A CYS* 4.3 1.8 - - + -
710A PHE 3.4 11.4 - - - +
711A TRP* 3.2 31.0 - - + -
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Residues in contact with ALA 701 (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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79A GLY 3.5 14.8 - - - +
80A THR* 3.4 18.6 - - - +
82A GLY* 3.6 15.3 - - - +
650A THR* 5.1 1.6 - - - +
653A SER* 5.2 1.6 + - - -
663A VAL* 4.4 2.6 - - - +
666A TYR* 2.7 34.0 + - - +
699A TYR* 3.9 6.7 + - + -
700A VAL* 1.3 70.9 - - - +
702A SER* 1.3 64.0 + - - +
710A PHE* 2.6 18.2 + - + +
712A GLY* 4.0 5.7 - - - +
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Residues in contact with SER 702 (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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80A THR* 2.9 21.8 + - - +
619A GLN* 2.5 48.3 + - - -
653A SER* 4.9 3.8 - - - -
663A VAL* 4.3 12.3 - - - -
700A VAL* 3.4 2.6 - - - +
701A ALA* 1.3 82.5 - - - +
703A CYS* 1.3 65.4 + - - +
710A PHE* 2.9 29.6 + - - -
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Residues in contact with CYS 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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253A VAL* 3.7 7.4 - - - -
619A GLN* 3.0 18.3 + - - +
653A SER* 5.5 0.2 + - - -
654A TYR 3.8 2.0 + - - +
655A GLY* 3.5 32.7 - - - +
661A PHE* 4.1 3.8 - - + -
663A VAL* 3.4 24.1 - - - +
700A VAL* 3.9 0.9 - - - -
702A SER* 1.3 75.0 - - - +
704A PHE* 1.3 62.0 + - - +
705A ASN 3.8 2.5 - - - +
708A GLY 2.9 8.7 - - - +
709A CYS* 2.0 48.9 - - - -
710A PHE* 5.0 0.2 - - - -
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Residues in contact with PHE 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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81A ARG* 5.8 1.8 - - - -
246A TRP* 3.6 47.1 - + - -
618A ALA* 4.0 8.6 - - + +
619A GLN* 3.5 24.2 - - - +
655A GLY 3.4 4.3 - - - -
656A ASP* 3.8 10.6 - - - -
657A PRO* 4.0 6.6 - - - +
703A CYS* 1.3 73.1 - - - +
705A ASN* 1.3 76.1 + - + +
707A TYR* 3.9 13.9 - + - -
708A GLY* 2.8 36.1 + - - -
710A PHE* 4.0 15.5 - + - -
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Residues in contact with ASN 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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655A GLY 2.9 16.0 + - - +
656A ASP* 3.5 15.2 - - - +
657A PRO* 4.3 11.5 - - - +
661A PHE* 4.3 0.2 - - - -
703A CYS* 3.8 5.5 - - - +
704A PHE* 1.3 97.3 + - + +
706A THR* 1.3 84.7 + - - +
707A TYR* 3.1 38.4 + - + -
708A GLY 2.8 23.2 + - - +
709A CYS* 4.2 0.2 - - - -
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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