Contacts of the strand formed by residues 705 - 712 (chain B) in PDB entry 4BIC
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 ARG 705 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B GLU* 3.8 25.7 + - - +
696B ALA* 5.1 2.2 - - - +
697B GLY 3.3 11.8 + - - +
698B ARG* 4.2 1.1 - - - +
703B GLN 3.6 0.6 + - - +
704B VAL* 1.3 84.4 - - - +
706B ILE* 1.3 63.7 + - - +
755B GLU* 5.0 1.7 - - - -
756B GLN* 3.9 45.9 + - + +
1942B GOL 3.3 45.1 + - - -
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Residues in contact with ILE 706 (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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671B LEU* 4.2 10.8 - - + -
673B TYR* 4.1 16.2 - - + -
697B GLY 2.9 44.3 + - - -
698B ARG* 3.8 6.3 - - - +
699B ASP* 4.6 10.5 - - + +
704B VAL* 4.1 8.7 - - + +
705B ARG* 1.3 78.5 - - - +
707B ALA* 1.3 58.4 + - - +
708B ILE* 3.8 12.1 - - + -
741B LEU* 3.9 25.1 - - + -
753B PHE* 3.3 38.1 - - + -
754B MET 3.5 7.0 - - - +
755B GLU* 5.4 0.4 - - - -
756B GLN* 3.2 12.5 - - - +
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Residues in contact with ALA 707 (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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2A IE4 3.4 37.7 - - + +
686B LEU* 3.8 17.5 - - + -
694B VAL* 4.1 5.6 - - + -
695B TYR 3.5 4.7 - - - -
706B ILE* 1.3 72.5 - - - +
708B ILE* 1.3 61.4 + - - +
709B LYS 4.1 0.9 - - - -
752B ILE 3.5 2.8 - - - +
753B PHE* 3.5 2.9 - - - -
754B MET* 2.7 36.9 + - + +
755B GLU 3.7 6.1 - - - +
756B GLN* 4.2 1.3 - - - +
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Residues in contact with ILE 708 (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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673B TYR* 3.8 21.3 - - + -
675B TYR* 3.6 28.5 - - + +
693B ILE 3.5 0.7 - - - +
694B VAL* 4.2 1.6 - - - -
695B TYR* 2.7 40.5 + - + +
696B ALA 4.6 0.2 - - - -
697B GLY* 3.8 26.2 - - - +
706B ILE* 3.8 7.9 - - + -
707B ALA* 1.3 75.5 - - - +
709B LYS* 1.3 61.2 + - - +
710B GLU* 3.5 18.0 + - + +
751B LYS* 3.9 28.7 - - + -
752B ILE 3.5 4.5 - - - +
753B PHE* 3.7 22.0 - - + -
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Residues in contact with LYS 709 (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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2A IE4 3.8 24.7 + - + +
689B GLY* 4.6 5.0 - - - -
690B THR 4.9 3.0 - - - +
691B TYR* 5.0 4.4 - - - +
692B GLY* 4.0 28.7 - - - +
693B ILE 3.5 5.6 - - - +
694B VAL* 3.8 18.8 - - + -
707B ALA 4.1 1.0 - - - -
708B ILE* 1.3 70.1 - - - +
710B GLU* 1.3 60.2 + - - +
711B ILE* 3.9 22.8 + - + +
750B ILE 3.3 2.1 - - - +
751B LYS* 3.3 6.1 - - - -
752B ILE* 2.9 45.8 + - + +
754B MET* 3.8 19.3 - - + +
822B ASP* 4.1 15.2 + - - -
824B GLY* 5.7 4.2 - - - +
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Residues in contact with GLU 710 (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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675B TYR* 2.5 34.5 + - - -
683B ARG* 2.9 30.2 + - - -
692B GLY* 3.6 2.1 - - - -
693B ILE* 2.8 34.6 + - - +
695B TYR* 3.5 16.6 + - + -
708B ILE* 3.5 4.9 + - + +
709B LYS* 1.3 70.3 - - - +
711B ILE* 1.3 62.9 + - - +
712B PRO* 4.0 4.7 - - - +
747B ASN* 4.9 2.1 + - - -
749B PHE* 4.1 30.1 - - + -
750B ILE 3.4 2.9 - - - -
751B LYS* 3.8 27.5 - - + -
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Residues in contact with ILE 711 (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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691B TYR* 4.1 20.4 - - + +
692B GLY* 4.3 9.0 - - - +
709B LYS* 4.2 23.6 - - + +
710B GLU* 1.3 74.6 - - - +
712B PRO* 1.3 79.0 - - + +
722B LEU* 5.1 17.7 - - + -
726B ILE* 5.6 0.9 - - + -
749B PHE* 3.5 2.3 - - - -
750B ILE* 2.7 52.4 + - + +
752B ILE* 3.5 30.1 - - + -
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Residues in contact with PRO 712 (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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691B TYR 3.9 12.8 - - - +
692B GLY* 5.1 0.4 - - - -
710B GLU 4.0 4.7 - - - +
711B ILE* 1.3 94.5 - - + +
713B GLU* 1.4 63.9 + - - +
714B ARG* 3.5 8.7 + - + +
748B GLY 3.9 3.8 - - - +
749B PHE* 3.6 28.2 - - + -
750B ILE* 4.7 0.9 - - - +
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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