Contacts of the helix formed by residues 787 - 806 (chain P) in PDB entry 1MVW
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 ILE 787 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783P LEU* 4.9 2.5 - - + +
786P ILE* 1.6 67.4 + - + +
788P THR* 1.3 58.9 + - - +
789P ALA* 3.0 3.3 - - - +
790P THR* 2.3 39.2 + - - +
791P GLN* 2.6 42.7 + - + +
110R VAL* 6.3 1.8 - - + -
114R LEU* 4.6 21.5 - - + +
115R GLY* 4.9 4.0 - - - -
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Residues in contact with THR 788 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783P LEU 3.6 2.4 + - - -
784P ALA* 2.3 23.4 + - - +
785P GLU* 2.6 20.0 - - - +
786P ILE 1.4 24.0 + - - -
787P ILE* 1.3 71.8 - - - +
789P ALA* 1.3 58.3 + - - -
791P GLN* 3.2 11.9 + - - +
792P ALA 3.2 10.7 + - - -
42R THR* 2.8 40.8 - - + +
44R ALA* 5.2 6.5 - - + -
116R GLU* 4.5 8.8 - - + +
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Residues in contact with ALA 789 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785P GLU 3.7 5.1 + - - +
786P ILE* 3.2 2.8 + - - +
787P ILE 3.0 2.8 - - - +
788P THR* 1.3 80.1 - - - +
790P THR* 1.3 63.8 + - - +
791P GLN 3.4 0.3 + - - -
792P ALA* 3.7 11.8 + - - +
793P ARG* 3.8 9.5 + - - +
42R THR* 4.1 1.8 - - - -
81R GLN* 3.2 48.8 + - + +
87R PHE* 4.4 8.2 - - + -
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Residues in contact with THR 790 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787P ILE* 2.3 32.8 + - - +
789P ALA* 1.3 70.8 - - - +
791P GLN* 1.3 62.2 + - + +
793P ARG* 4.4 2.6 - - + +
794P CYS* 2.7 41.1 + - - -
86R ASP* 5.1 2.8 + - - +
87R PHE* 3.1 40.8 - - + -
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Residues in contact with GLN 791 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787P ILE* 2.6 37.2 + - + +
788P THR* 3.5 11.2 + - - +
789P ALA 3.1 0.2 - - - -
790P THR* 1.3 74.9 - - - +
792P ALA* 1.3 55.2 - - - +
794P CYS* 2.7 40.3 + - - +
795P ARG* 3.0 8.3 + - - -
111R LEU* 5.7 7.1 + - + +
114R LEU 2.1 34.6 + - - -
115R GLY* 3.0 5.1 - - - -
116R GLU* 2.3 63.1 + - + +
118R MET* 4.6 4.3 - - + -
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Residues in contact with ALA 792 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788P THR 3.2 3.0 + - - +
789P ALA* 3.7 5.4 - - - +
791P GLN* 1.3 76.5 - - - +
793P ARG* 1.3 51.6 + - - +
795P ARG* 2.8 5.2 + - - +
796P GLY* 2.5 35.0 + - - -
35R ARG* 3.3 12.7 + - - +
40R ASN* 3.6 13.0 - - - +
41R PRO 3.8 0.4 - - - -
42R THR* 2.7 51.1 - - + +
81R GLN* 5.1 1.3 - - - +
116R GLU* 4.2 1.4 + - - -
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Residues in contact with ARG 793 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789P ALA 3.8 10.6 + - - +
790P THR* 4.4 3.8 - - + +
791P GLN 3.4 0.6 - - - -
792P ALA* 1.3 74.1 - - - +
794P CYS* 1.3 57.8 + - - +
796P GLY* 2.9 2.1 + - - -
797P PHE* 2.4 42.0 + - + +
800P ARG* 4.4 11.0 - - - +
40R ASN* 1.6 64.9 - - + +
79R LYS* 5.9 2.0 + - - +
82R GLY* 4.4 23.6 + - - -
87R PHE* 4.4 23.3 - - + -
146R ILE* 5.1 10.1 - - + -
147R MET* 4.2 35.3 - - + +
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Residues in contact with CYS 794 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790P THR* 2.7 35.7 - - - -
791P GLN* 2.7 17.0 + - - +
793P ARG* 1.3 78.3 - - - +
795P ARG* 1.3 49.7 + - - +
797P PHE* 2.9 10.5 + - - +
798P LEU* 2.4 42.3 + - + +
111R LEU* 4.7 22.7 - - + -
118R MET* 4.8 4.0 - - + -
126R LEU* 5.5 5.8 - - + -
146R ILE* 5.2 7.9 - - + -
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Residues in contact with ARG 795 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791P GLN 3.0 9.0 + - - +
792P ALA 2.8 5.2 + - - +
794P CYS* 1.3 70.7 - - - +
796P GLY* 1.3 66.2 - - - +
798P LEU* 2.9 13.4 + - - +
799P MET* 3.1 10.2 + - - +
35R ARG* 2.4 50.1 + - - +
43R ASN* 1.7 87.5 + - - +
116R GLU* 1.6 65.3 + - - +
117R LYS 4.0 3.1 + - - +
118R MET* 2.1 56.7 - - + +
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Residues in contact with GLY 796 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792P ALA 2.5 15.8 + - - -
793P ARG 3.2 2.9 - - - -
795P ARG* 1.3 79.2 - - - +
797P PHE* 1.3 53.7 + - - +
798P LEU 2.8 0.5 + - - -
799P MET* 2.7 22.2 + - - +
800P ARG* 3.1 13.9 + - - +
35R ARG* 2.8 35.1 - - - +
40R ASN* 3.9 8.3 - - - -
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Residues in contact with PHE 797 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793P ARG* 2.4 22.6 + - - +
794P CYS* 3.0 6.7 - - - +
796P GLY* 1.3 70.4 - - - -
798P LEU* 1.3 76.8 + - + +
800P ARG* 3.2 29.8 + - - +
801P VAL* 3.4 21.9 + - + +
126R LEU* 2.8 20.9 - - + -
130R GLN* 5.6 0.9 - - - -
145R HIS 3.5 6.1 - - - -
146R ILE* 2.4 72.9 - - + +
149R VAL* 2.3 41.3 - - + -
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Residues in contact with LEU 798 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794P CYS* 2.4 21.8 + - + +
795P ARG* 3.3 11.4 - - - +
796P GLY 2.8 2.2 + - - -
797P PHE* 1.3 88.7 - - + +
799P MET* 1.3 62.0 + - + +
801P VAL* 3.4 11.6 + - - +
802P GLU* 3.7 10.0 + - - +
111R LEU* 5.2 0.2 - - + -
118R MET* 5.1 13.9 - - + -
122R GLU* 3.3 42.2 - - + +
123R VAL* 4.6 0.4 - - - +
125R GLU* 5.7 1.6 - - + +
126R LEU* 2.0 85.2 - - + -
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Residues in contact with MET 799 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795P ARG 3.1 7.5 + - - +
796P GLY 2.7 11.2 + - - +
798P LEU* 1.3 72.0 - - + +
800P ARG* 1.3 58.6 + - - +
801P VAL 2.9 5.2 - - - -
802P GLU* 2.8 38.2 + - + +
803P TYR* 3.0 12.6 + - - +
806P MET* 5.6 8.1 - - - -
32R ASP* 2.6 65.7 - - + +
35R ARG* 5.1 4.3 - - + +
36R ALA* 6.0 2.0 - - - +
122R GLU* 5.3 8.1 - - - +
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Residues in contact with ARG 800 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793P ARG* 4.4 6.5 - - - +
796P GLY* 3.1 6.8 + - - +
797P PHE* 3.2 41.2 + - - +
799P MET* 1.3 77.5 - - - +
801P VAL* 1.3 56.3 + - - +
802P GLU 3.3 0.2 - - - -
803P TYR* 3.8 8.0 + - + +
804P ARG* 3.8 15.9 + - - +
35R ARG* 3.0 31.5 + - - +
36R ALA* 4.4 9.2 - - - +
38R GLY* 4.7 9.2 - - - +
39R GLN 4.2 3.8 + - - +
40R ASN* 1.6 46.8 + - - +
146R ILE 4.9 0.6 + - - -
149R VAL* 3.2 56.1 + - + +
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Residues in contact with VAL 801 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797P PHE* 3.4 42.4 - - + +
798P LEU 3.4 6.5 + - - +
799P MET 2.9 1.0 - - - -
800P ARG* 1.3 77.0 - - - +
802P GLU* 1.3 75.1 + - - +
803P TYR 3.3 0.7 - - - -
804P ARG* 3.4 12.5 + - + +
805P ALA* 3.3 18.8 + - + +
808P GLU* 5.0 2.4 - - - +
125R GLU 5.9 3.1 - - - +
126R LEU* 4.9 4.5 - - + -
149R VAL* 4.3 7.9 - - + -
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Residues in contact with GLU 802 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798P LEU 3.7 5.0 + - - +
799P MET* 2.8 31.9 + - + +
801P VAL* 1.3 88.4 - - - +
803P TYR* 1.3 65.1 + - - +
805P ALA* 3.2 10.9 + - - +
806P MET* 2.8 34.0 + - + +
809P ARG* 3.0 41.5 + - - +
125R GLU* 5.3 13.6 - - - +
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Residues in contact with TYR 803 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799P MET 3.0 12.0 + - - +
800P ARG* 4.2 6.7 - - - +
801P VAL 3.3 0.4 - - - -
802P GLU* 1.3 77.2 - - - +
804P ARG* 1.3 48.7 + - - +
806P MET* 3.4 13.6 - - + +
807P VAL* 2.1 70.2 + - + +
13R ALA* 5.0 4.1 - - + +
16R LEU* 3.3 33.6 - - + +
17R PHE* 2.8 51.3 - + + -
36R ALA* 4.7 13.0 - - + -
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Residues in contact with ARG 804 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800P ARG 3.8 8.7 + - - +
801P VAL* 3.4 19.9 + - + +
802P GLU 3.2 0.6 - - - -
803P TYR* 1.3 73.4 - - - +
805P ALA* 1.3 51.5 + - - +
807P VAL* 3.2 13.7 - - + +
808P GLU* 2.3 50.9 + - + +
148R SER 4.4 6.1 + - - -
149R VAL* 4.4 35.7 - - - +
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Residues in contact with ALA 805 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801P VAL* 3.3 9.8 + - + +
802P GLU* 3.2 18.3 + - - +
803P TYR 3.1 0.2 - - - -
804P ARG* 1.3 77.7 - - - +
806P MET* 1.3 48.4 + - - +
807P VAL 2.5 5.9 - - - -
808P GLU* 2.3 24.4 + - + +
809P ARG* 1.8 59.2 + - + +
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Residues in contact with MET 806 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799P MET* 5.6 7.9 - - - -
802P GLU* 2.8 33.1 + - + +
803P TYR* 3.4 22.7 - - + +
805P ALA* 1.3 70.7 - - - +
807P VAL* 1.9 46.8 - - + +
809P ARG* 3.1 28.3 - - - +
810P ARG* 2.5 35.9 + - - +
813P ILE* 5.2 2.6 - - - +
17R PHE* 5.1 10.3 - - + -
19R ARG* 5.6 7.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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