Contacts of the helix formed by residues 775 - 789 (chain H) in PDB entry 2VE8
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 GLY 775 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804D ILE 5.6 1.1 - - - -
769H GLN* 3.8 2.9 - - - -
774H ILE* 1.3 81.1 - - - +
776H TYR* 1.3 67.3 + - - -
777H ASN 3.4 2.2 - - - -
778H ARG* 3.4 9.7 + - - +
779H ALA* 3.0 22.0 + - - +
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Residues in contact with TYR 776 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761D ARG* 3.4 58.7 - - + +
803D VAL 4.9 2.9 - - - +
804D ILE 5.0 1.2 + - - +
807D ALA* 5.3 3.6 - - + -
797F THR* 2.6 29.6 + - - -
798F ASN* 2.7 35.5 + - + +
765H ILE* 3.9 20.4 - - + +
769H GLN* 3.3 31.4 - - - +
775H GLY* 1.3 70.9 - - - -
777H ASN* 1.3 78.1 + - - +
779H ALA* 3.2 2.6 + - - +
780H ALA* 2.8 33.0 + - + +
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Residues in contact with ASN 777 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D GLU* 5.6 1.6 - - - +
775H GLY 3.4 0.6 - - - -
776H TYR* 1.3 101.5 - - - +
778H ARG* 1.3 57.7 + - - +
780H ALA* 3.3 5.4 + - - +
781H ARG* 3.0 47.8 + - + +
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Residues in contact with ARG 778 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747H ASP* 2.7 40.2 + - - +
748H PRO* 4.4 10.5 - - - +
749H LEU* 3.6 24.9 - - - +
774H ILE* 4.1 24.7 - - + +
775H GLY* 3.4 14.3 + - - +
776H TYR 3.2 0.2 - - - -
777H ASN* 1.3 77.6 - - - +
779H ALA* 1.3 62.4 + - - +
781H ARG* 3.3 31.1 + - - +
782H MET* 3.1 31.0 + - + +
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Residues in contact with ALA 779 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765H ILE* 3.8 15.0 - - + +
768H VAL* 4.1 11.4 - - + +
769H GLN* 3.6 23.6 - - + -
774H ILE* 3.9 16.5 - - + +
775H GLY 3.0 16.8 + - - +
776H TYR 3.6 2.2 - - - +
778H ARG* 1.3 76.4 - - - +
780H ALA* 1.3 63.0 + - - +
782H MET* 3.1 4.7 + - - +
783H ILE* 3.0 26.7 + - - +
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Residues in contact with ALA 780 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797F THR* 4.6 11.7 - - + -
765H ILE* 3.5 30.6 - - + +
776H TYR* 2.8 25.8 + - + +
777H ASN* 3.6 10.8 - - - +
778H ARG 3.3 0.2 - - - -
779H ALA* 1.3 77.3 - - - +
781H ARG* 1.3 57.3 + - + +
783H ILE* 3.4 2.6 + - - +
784H GLU* 3.0 28.6 + - - +
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Residues in contact with ARG 781 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747H ASP* 5.0 4.0 + - - -
777H ASN* 3.0 38.7 + - + +
778H ARG* 3.3 39.1 + - - +
780H ALA* 1.3 75.7 - - + +
782H MET* 1.3 59.6 + - + +
784H GLU* 3.4 14.4 + - - +
785H ALA* 2.9 28.9 + - - +
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Residues in contact with MET 782 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747H ASP* 3.2 38.6 - - + +
749H LEU* 3.6 17.7 - - + -
750H TYR* 3.6 36.2 - - + -
753H ALA* 4.0 10.5 - - + -
768H VAL* 4.9 3.8 - - + -
772H LEU* 4.2 2.2 - - + -
774H ILE* 3.8 25.8 - - + -
778H ARG* 3.1 16.3 + - + +
779H ALA* 3.1 10.3 + - - +
781H ARG* 1.3 76.1 - - + +
783H ILE* 1.3 61.2 + - - +
785H ALA* 3.2 7.9 + - - +
786H MET* 2.8 44.4 + - + +
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Residues in contact with ILE 783 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797F THR 6.0 0.2 - - - +
757H VAL* 4.5 1.1 - - + -
763H ALA* 4.1 9.9 - - + -
764H SER* 4.0 19.5 - - - +
765H ILE* 4.1 28.7 - - + +
768H VAL* 4.0 23.1 - - + -
779H ALA 3.0 19.2 + - - +
780H ALA 3.4 4.5 + - - +
782H MET* 1.3 77.3 - - - +
784H GLU* 1.3 62.3 + - - +
786H MET* 3.1 21.3 + - - +
787H GLU* 3.0 19.8 + - - +
792H VAL* 3.9 5.1 - - + +
801H ARG* 3.4 38.6 - - - +
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Residues in contact with GLU 784 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780H ALA 3.0 17.0 + - - +
781H ARG* 3.7 12.9 - - - +
783H ILE* 1.3 75.3 - - - +
785H ALA* 1.3 57.4 + - - +
787H GLU* 3.0 13.3 + - + +
788H MET* 2.9 52.9 + - + +
801H ARG* 5.1 6.5 - - - +
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Residues in contact with ALA 785 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750H TYR* 3.7 21.4 + - + -
781H ARG 2.9 15.1 + - - +
782H MET* 3.2 10.5 + - - +
784H GLU* 1.3 74.5 - - - +
786H MET* 1.3 57.6 + - - +
788H MET* 3.2 20.7 + - + +
789H ALA* 2.9 29.8 + - - +
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Residues in contact with MET 786 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750H TYR* 3.7 18.8 - - + +
753H ALA* 3.6 42.0 - - + +
754H VAL* 3.9 14.6 - - + +
757H VAL* 3.9 32.1 - - + -
768H VAL* 4.8 1.6 - - + -
782H MET* 2.8 27.5 + - + +
783H ILE* 3.1 16.4 + - + +
785H ALA* 1.3 79.4 - - - +
787H GLU* 1.3 60.6 + - - +
789H ALA 3.4 0.7 + - - -
790H GLY 3.1 3.3 + - - -
791H VAL* 2.9 40.6 + - + +
792H VAL* 3.5 14.7 + - + -
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Residues in contact with GLU 787 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783H ILE 3.0 9.1 + - - +
784H GLU* 3.0 13.0 + - + +
786H MET* 1.3 72.5 - - - +
788H MET* 1.3 70.2 + - + +
790H GLY* 3.0 13.3 + - - -
792H VAL* 3.6 19.8 - - + +
794H PRO* 3.6 34.5 - - + +
795H MET 4.5 0.3 + - - -
801H ARG* 2.8 39.6 + - - +
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Residues in contact with MET 788 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784H GLU* 2.9 33.5 + - + +
785H ALA* 3.2 26.0 + - + +
787H GLU* 1.3 82.6 - - + +
789H ALA* 1.3 58.2 + - - +
790H GLY 3.5 0.3 + - - -
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Residues in contact with ALA 789 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750H TYR* 3.9 14.1 - - - +
785H ALA 2.9 16.7 + - - +
786H MET 3.9 3.8 - - - +
787H GLU 3.2 0.4 - - - -
788H MET* 1.3 76.6 - - - +
790H GLY* 1.3 61.3 + - - +
791H VAL* 3.3 11.6 + - + +
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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