Contacts of the helix formed by residues 780 - 789 (chain A) in PDB entry 3MP1
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 LYS 780 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750A ASN* 5.8 1.6 + - - -
778A PRO 3.6 1.0 + - - -
779A ASP* 1.3 79.2 - - + +
781A LEU* 1.3 62.9 - - - +
782A GLU* 3.0 24.2 + - - +
783A GLU* 2.9 37.1 + - + +
784A LYS* 3.3 12.7 + - + +
891A GLU* 5.8 2.4 + - - -
1082A ARG* 5.2 8.5 - - - +
1121A PRO* 6.1 5.4 - - - -
1193A LYS* 6.0 6.1 - - - +
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Residues in contact with LEU 781 (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 TRP* 3.8 25.8 - - + -
749A ILE* 3.4 43.5 - - - +
750A ASN* 3.5 11.7 - - + +
778A PRO* 3.6 20.8 + - + +
779A ASP 3.1 4.8 - - - -
780A LYS* 1.3 75.5 - - - +
782A GLU* 1.3 70.2 + - - +
783A GLU 3.1 0.2 + - - -
784A LYS* 4.5 3.4 - - - +
785A PHE* 3.0 29.1 + - - +
798A ILE* 4.1 27.4 - - + -
799A PHE 4.3 2.7 - - - +
800A TRP* 3.8 24.9 - - + -
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Residues in contact with GLU 782 (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 ASN* 5.4 0.7 - - - +
780A LYS* 3.0 27.8 - - - +
781A LEU* 1.3 81.2 + - - +
783A GLU* 1.3 69.6 + - + +
786A PRO* 3.3 12.9 - - - +
800A TRP* 3.5 36.6 - - + -
804A ARG* 3.8 39.4 + - - +
808A TYR* 2.9 24.5 + - - +
891A GLU* 5.6 2.4 - - - +
2B GLC 5.0 2.9 + - - -
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Residues in contact with GLU 783 (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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780A LYS* 2.9 30.4 + - + +
782A GLU* 1.3 89.5 - - + +
784A LYS* 1.3 61.8 + - + +
785A PHE 3.4 0.7 - - - -
786A PRO* 3.3 15.1 - - - +
787A GLN* 3.0 28.2 + - - +
804A ARG* 6.0 4.0 - - - +
1079A TYR* 2.7 40.3 + - + +
1082A ARG* 4.5 7.8 + - - -
1121A PRO* 6.0 2.1 - - - +
1122A ASN* 4.2 16.7 + - - +
1123A ALA* 4.4 4.3 - - - +
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Residues in contact with LYS 784 (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 TRP* 4.1 20.2 - - + -
778A PRO* 4.5 13.6 - - + +
779A ASP* 3.2 27.4 + - - +
780A LYS* 3.8 11.4 - - + +
781A LEU* 3.2 7.1 + - - +
783A GLU* 1.3 79.8 - - + +
785A PHE* 1.3 65.6 + - - +
786A PRO 3.3 0.7 - - - -
787A GLN* 3.2 6.4 + - - +
788A VAL* 3.1 35.6 + - + +
1118A GLU* 3.7 24.6 + - - -
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Residues in contact with PHE 785 (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 TRP* 3.9 8.2 - + + -
781A LEU 3.0 15.9 + - - +
784A LYS* 1.3 77.8 - - - +
786A PRO* 1.3 63.8 - - + +
788A VAL* 4.4 1.6 - - - -
789A ALA* 2.8 57.2 + - + +
795A PRO* 3.8 38.1 - - + -
797A ILE 5.9 0.2 - - - -
798A ILE* 3.4 34.8 - - + -
808A TYR* 4.0 22.9 - + - +
813A LEU* 4.1 12.1 - - + -
814A LEU* 3.9 29.8 - - + -
1005A ASN* 3.9 16.8 - - + -
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Residues in contact with PRO 786 (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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782A GLU 3.3 11.9 - - - +
783A GLU* 3.3 17.9 - - - +
785A PHE* 1.3 96.1 - - + +
787A GLN* 1.3 60.4 + - + +
789A ALA 4.6 0.7 - - - -
790A ALA* 4.6 8.7 - - - +
808A TYR* 3.5 28.5 - - + -
813A LEU* 3.8 24.3 - - + +
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Residues in contact with GLN 787 (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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783A GLU* 3.0 26.8 + - - +
784A LYS* 3.2 9.5 + - - +
786A PRO* 1.3 82.3 - - + +
788A VAL* 1.3 65.9 + - + +
790A ALA* 4.9 2.4 - - - +
791A THR* 4.3 10.6 + - - +
1112A SER* 4.2 16.7 + - - +
1113A SER 4.1 0.3 - - - +
1114A TYR 5.3 0.7 - - - +
1116A THR* 3.4 14.9 - - - +
1122A ASN* 3.3 30.4 + - - +
1123A ALA* 5.7 1.0 - - - +
1180A ARG* 4.1 19.8 + - - +
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Residues in contact with VAL 788 (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 TRP* 4.1 18.4 - - + -
784A LYS* 3.1 28.5 + - + +
785A PHE* 4.1 3.4 - - - +
787A GLN* 1.3 85.3 - - + +
789A ALA* 1.3 65.9 + - - +
790A ALA 3.4 1.6 - - - -
791A THR* 2.7 28.7 - - - +
793A ASP* 3.0 22.5 - - - +
794A GLY* 3.6 20.2 - - - -
795A PRO* 4.6 0.4 - - + -
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Residues in contact with ALA 789 (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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785A PHE* 2.8 46.1 + - + +
788A VAL* 1.3 80.8 - - - +
790A ALA* 1.3 57.4 + - - +
792A GLY* 3.1 12.8 + - - -
793A ASP 2.8 21.9 + - - +
794A GLY* 4.2 0.9 - - - -
813A LEU* 4.2 10.1 - - + -
1005A ASN* 3.6 18.2 - - - +
1007A ALA* 3.6 10.7 - - - +
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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