Contacts of the strand formed by residues 749 - 757 (chain A) in PDB entry 2VJ0
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 749 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721A LEU* 3.3 23.8 - - + -
722A LEU* 4.3 12.3 - - + -
743A ASN* 3.3 46.7 - - + -
745A THR* 4.0 3.4 - - + -
747A THR 3.9 0.2 - - - -
748A GLN* 1.3 78.4 - - - +
750A LEU* 1.3 62.9 + - - +
752A PHE* 3.9 24.2 - + + -
775A PRO 3.5 1.3 - - - +
776A THR* 3.4 5.7 - - - +
777A VAL* 2.8 41.0 + - + +
805A PHE* 3.5 45.8 - + + -
806A ARG 3.3 3.4 - - - -
807A TYR* 3.7 23.1 - + - -
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Residues in contact with LEU 750 (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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748A GLN* 3.9 27.8 - - + +
749A PHE* 1.3 79.7 - - - +
751A ASN* 1.3 76.3 + - - +
752A PHE 3.0 3.1 + - - -
775A PRO 3.6 1.3 - - - -
776A THR* 3.9 19.3 - - + +
805A PHE* 3.5 1.2 - - - -
806A ARG* 2.8 59.5 + - + +
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Residues in contact with ASN 751 (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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750A LEU* 1.3 74.7 - - - +
752A PHE* 1.3 57.8 + - - +
753A THR* 2.8 23.1 + - - +
775A PRO* 3.0 19.5 + - - +
776A THR* 5.4 0.2 + - - -
804A GLN* 3.3 8.1 - - - +
805A PHE* 3.8 2.0 - - - -
806A ARG* 3.0 42.0 - - + +
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Residues in contact with PHE 752 (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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722A LEU* 4.3 7.2 - - + -
741A TYR* 3.7 38.1 - + + -
749A PHE* 3.9 24.5 - + + -
750A LEU 3.0 0.8 - - - -
751A ASN* 1.3 73.5 - - - +
753A THR* 1.3 58.6 + - - +
754A PRO* 3.5 27.5 - - + +
773A VAL* 4.4 13.1 - - + +
774A ASP 4.2 2.0 - - - +
775A PRO* 2.8 32.6 + - - +
777A VAL* 3.6 23.3 - - + -
783A VAL* 4.6 2.2 - - + -
803A ILE* 3.6 26.2 - - + -
804A GLN 3.5 3.4 - - - -
805A PHE* 3.7 31.0 - + + -
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Residues in contact with THR 753 (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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751A ASN* 2.8 23.0 + - - +
752A PHE* 1.3 75.8 + - - +
754A PRO* 1.3 63.1 - - - +
755A THR* 3.8 16.7 + - - +
775A PRO* 5.5 1.0 - - - +
802A ASN* 3.5 4.9 - - - +
803A ILE* 4.4 0.4 - - - -
804A GLN* 2.8 38.4 + - - +
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Residues in contact with PRO 754 (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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741A TYR* 3.2 35.0 - - + +
752A PHE* 3.5 33.2 - - + +
753A THR* 1.3 90.2 - - + +
755A THR* 1.3 59.9 + - - +
773A VAL* 4.5 15.6 - - + +
785A GLN* 3.7 15.7 + - - +
801A LEU* 4.3 5.6 - - + -
802A ASN 3.3 6.7 - - - +
803A ILE* 4.3 4.3 - - + -
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Residues in contact with THR 755 (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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753A THR* 4.0 17.0 + - - +
754A PRO* 1.3 76.9 + - - +
756A LEU* 1.3 68.1 + - - +
757A ILE* 3.7 21.7 + - + -
800A VAL 3.5 2.9 - - - +
801A LEU* 3.5 4.5 - - - +
802A ASN* 2.8 43.6 + - - +
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Residues in contact with LEU 756 (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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754A PRO 6.1 0.4 - - - -
755A THR* 1.3 77.8 - - - +
757A ILE* 1.3 61.3 + - - +
758A CYS* 4.1 3.3 + - - -
768A LEU* 4.2 26.5 - - + +
770A THR* 3.9 24.0 - - + -
785A GLN* 5.2 3.1 - - - +
787A ILE* 3.2 45.8 - - + -
799A PRO* 5.3 2.0 - - + -
800A VAL 3.6 2.7 - - - +
801A LEU* 4.0 21.1 - - + -
818A LEU* 3.7 21.8 - - + -
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Residues in contact with ILE 757 (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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694A LEU* 3.9 31.0 - - + -
755A THR* 3.8 19.1 - - + +
756A LEU* 1.3 75.1 - - - +
758A CYS* 1.3 68.9 + - - +
798A ALA 4.7 0.3 - - - +
799A PRO* 3.5 2.9 - - - +
800A VAL* 2.8 56.5 + - + +
802A ASN* 3.8 27.1 - - + -
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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