Contacts of the strand formed by residues 673 - 678 (chain A) in PDB entry 5C58
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 ASN 673 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A THR 4.1 2.7 - - - -
609A TYR* 4.0 11.9 - - + -
659A ILE 3.7 0.2 - - - -
660A ASP 3.5 5.7 + - - -
661A ARG* 3.1 50.0 + - + +
662A ASN* 4.0 1.8 - - - +
663A LYS* 3.3 44.6 - - - +
668A GLN* 5.4 1.0 + - - -
670A SER* 3.4 25.6 + - - +
672A GLY* 1.3 74.2 - - - +
674A ALA* 1.3 60.3 + - - +
720A TRP* 4.7 2.7 - - + -
39B ASP* 3.5 22.9 - - - +
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Residues in contact with ALA 674 (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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606A SER* 4.0 11.9 - - - +
607A THR 3.0 16.7 + - - +
608A GLN* 3.2 8.2 - - + -
609A TYR* 2.8 27.8 + - - +
657A LEU* 3.7 21.3 - - + -
658A ALA 3.2 11.4 - - - +
659A ILE* 4.0 11.0 - - + -
661A ARG* 5.1 0.2 - - - -
672A GLY 3.1 1.8 + - - +
673A ASN* 1.3 74.1 - - - +
675A ALA* 1.3 63.4 + - - +
720A TRP* 5.6 0.2 - - - -
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Residues in contact with ALA 675 (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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608A GLN* 5.2 1.1 - - - +
609A TYR 3.5 18.4 - - - +
610A PRO 4.7 0.4 - - - +
657A LEU* 4.3 3.3 - - - +
658A ALA* 2.9 31.6 + - - +
661A ARG* 4.6 3.3 - - + +
674A ALA* 1.3 77.7 - - - +
676A TYR* 1.3 68.4 + - - +
677A VAL* 3.6 5.5 + - + +
720A TRP* 3.6 42.6 - - + +
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Residues in contact with TYR 676 (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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170A TYR* 3.0 35.2 + + - -
187A SER* 5.4 1.2 + - - -
193A ASN* 4.0 12.4 + - - -
594A THR* 4.5 4.0 - - + +
595A GLU* 3.4 50.6 + - + +
598A THR* 4.3 10.5 - - + -
608A GLN* 4.3 14.8 + - + -
609A TYR 4.4 2.8 + - - -
611A ASN* 2.6 33.7 + - - +
614A LEU* 3.3 6.3 - - + +
655A ILE* 4.0 7.2 - - + -
656A ASN* 3.3 13.0 - - - -
657A LEU* 3.4 55.5 - - + +
675A ALA* 1.3 74.4 - - - +
677A VAL* 1.3 54.4 + - - +
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Residues in contact with VAL 677 (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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611A ASN* 3.9 4.0 - - - +
614A LEU* 3.8 7.9 - - - -
655A ILE* 3.5 2.5 - - - -
656A ASN 3.0 24.0 + - - +
658A ALA* 3.8 15.7 - - + -
661A ARG* 4.6 9.2 - - - +
675A ALA 4.1 6.3 - - - +
676A TYR* 1.3 79.9 - - - +
678A ASN* 1.3 64.6 + - - +
714A PHE* 3.4 28.8 - - + -
716A SER* 3.6 18.6 - - - -
717A ASN 5.9 0.9 - - - +
720A TRP* 3.6 33.7 - - + -
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Residues in contact with ASN 678 (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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611A ASN* 5.1 0.2 - - - +
613A PHE 4.4 1.6 - - - +
614A LEU* 3.4 14.1 - - - +
615A GLN* 2.9 61.9 + - - +
653A ASN* 2.7 30.7 + - - +
654A TYR 4.1 1.1 - - - -
655A ILE* 3.4 10.9 - - - +
677A VAL* 1.3 81.1 - - - +
679A ASN* 1.3 64.4 + - - +
680A LEU* 3.5 11.2 + - + +
714A PHE* 4.3 1.3 - - - -
715A CYS 3.8 5.9 - - - +
716A SER* 4.5 2.9 - - - -
717A ASN* 5.5 1.7 + - - -
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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