Contacts of the strand formed by residues 670 - 676 (chain A) in PDB entry 2IVF
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 PHE 670 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 3.6 12.6 - - - -
91A SER* 3.2 52.4 + - - -
112A THR* 3.5 28.7 - - + -
122A TYR* 3.7 18.6 - + - -
125A LEU* 3.7 16.2 - - + -
664A PRO* 3.2 9.6 - - - +
668A ASN* 3.0 20.3 + - + -
669A PRO* 1.3 96.9 - - + +
671A PHE* 1.3 61.1 + - - +
672A THR* 4.3 1.6 - - - -
767A GLN* 3.9 11.7 - - - +
768A THR 3.2 13.9 - - - +
769A ARG* 3.9 10.5 - - + +
770A PHE* 3.9 3.0 - - - +
1977A MES 3.6 13.9 - - - +
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Residues in contact with PHE 671 (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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484A SER* 4.3 19.1 - - - -
487A ASN* 4.3 11.4 - - - -
661A MET* 3.6 26.0 - - + -
662A THR* 3.3 22.7 - - - -
663A THR* 4.7 1.3 - - - -
664A PRO* 3.5 28.9 - - + -
670A PHE* 1.3 73.3 - - - +
672A THR* 1.3 61.7 + - - +
747A ASN* 3.8 16.4 - - - -
752A VAL* 3.5 24.2 - - + -
753A PHE* 3.7 31.0 - + + -
762A PHE* 3.6 2.8 - - + -
767A GLN* 3.1 5.0 - - - +
768A THR 2.8 31.2 + - - +
770A PHE* 3.8 18.6 - + + -
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Residues in contact with THR 672 (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 SER* 3.8 13.7 - - - -
91A SER* 2.7 24.7 + - - -
93A LYS* 3.7 29.6 - - + +
661A MET* 3.2 5.9 - - - -
662A THR* 2.8 43.2 + - - +
670A PHE* 4.3 2.1 - - - -
671A PHE* 1.3 76.5 - - - +
673A PHE* 1.3 74.1 + - - +
674A VAL* 4.3 0.2 - - - +
762A PHE* 3.6 3.6 - - - -
766A GLY 3.4 11.4 - - - +
767A GLN* 3.4 12.3 + - - +
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Residues in contact with PHE 673 (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 TRP* 3.8 35.1 - + + +
80A GLY 4.0 4.9 - - - -
659A HIS* 4.3 2.2 - + - -
660A GLU 3.8 1.1 - - - -
672A THR* 1.3 83.1 - - - +
674A VAL* 1.3 72.7 + - - +
675A ASP* 3.7 41.5 - - + -
740A LEU* 3.5 31.2 - - + -
759A TYR* 3.6 14.4 - + - -
762A PHE* 3.4 35.0 - + + +
763A LYS* 3.4 37.7 - - + -
766A GLY* 2.8 17.4 + - - +
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Residues in contact with VAL 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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79A TRP 4.1 1.6 - - - -
80A GLY* 4.3 1.8 - - - -
81A SER* 3.6 46.2 - - - +
83A LEU* 3.9 27.1 - - + -
656A TYR* 3.8 23.1 - - - +
658A LYS 4.0 6.7 - - - +
659A HIS* 3.2 6.8 - - - -
660A GLU* 2.9 43.6 + - + +
672A THR 4.3 4.3 - - - +
673A PHE* 1.3 81.4 - - - +
675A ASP* 1.3 68.9 + - - +
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Residues in contact with ASP 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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78A ASN* 3.1 34.3 + - + +
79A TRP* 3.0 23.5 + - - +
656A TYR* 3.3 20.1 - - - +
658A LYS 3.7 4.2 - - - +
659A HIS* 3.6 16.5 + - - -
673A PHE* 3.7 25.4 - - + -
674A VAL* 1.3 76.2 - - - +
676A ARG* 1.3 80.1 + - - +
677A SER* 3.3 7.0 + - - +
763A LYS* 5.7 1.7 - - - +
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Residues in contact with ARG 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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76A LYS* 4.5 3.5 + - - -
78A ASN* 4.9 0.7 + - - -
656A TYR 3.6 3.6 - - - -
657A GLU 3.6 22.2 + - - +
658A LYS* 4.0 5.4 - - - +
659A HIS* 3.5 41.0 - - + +
675A ASP* 1.3 83.4 + - - +
677A SER* 1.3 62.8 + - - +
678A VAL 3.7 7.4 - - - +
679A ALA* 3.6 25.0 - - - +
680A PRO* 3.5 20.4 - - - +
686A GLU* 4.7 7.7 + - - -
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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