Contacts of the helix formed by residues 787 - 806 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783M LEU 3.8 6.3 - - - +
784M ALA* 3.4 11.0 - - - +
785M GLU 2.4 5.6 + - - +
786M ILE* 1.2 104.0 + - + +
788M THR* 1.3 55.3 + - - +
789M ALA* 3.0 4.3 - - - +
790M THR* 2.4 39.4 + - - +
791M GLN* 2.6 47.8 + - + +
114O LEU* 4.9 13.2 - - + +
115O GLY* 5.0 3.1 - - - -
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Residues in contact with THR 788 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784M ALA* 2.5 25.6 + - - +
785M GLU* 2.1 40.2 + - + +
787M ILE* 1.3 71.6 - - - +
789M ALA* 1.3 54.4 + - - +
791M GLN* 3.2 10.7 + - - +
792M ALA 3.2 8.3 + - - -
42O THR* 2.5 49.4 - - + +
44O ALA* 5.0 8.3 - - + -
116O GLU* 4.7 6.0 - - - +
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Residues in contact with ALA 789 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785M GLU 3.8 3.1 + - - +
787M ILE 3.0 2.6 - - - +
788M THR* 1.3 79.5 - - - +
790M THR* 1.3 63.0 + - - +
791M GLN 3.4 0.2 + - - -
792M ALA* 3.7 11.6 + - - +
793M ARG* 3.8 9.9 + - - +
42O THR* 3.9 1.6 - - - -
81O GLN* 2.9 54.5 + - + +
87O PHE* 4.7 5.0 - - + -
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Residues in contact with THR 790 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786M ILE 5.1 0.6 + - - -
787M ILE* 2.4 32.6 + - - +
789M ALA* 1.3 70.6 - - - +
791M GLN* 1.3 61.2 + - + -
793M ARG* 4.4 1.5 - - - +
794M CYS* 2.7 40.3 + - - -
86O ASP* 5.4 2.9 + - - +
87O PHE* 3.3 38.2 - - + -
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Residues in contact with GLN 791 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787M ILE* 2.6 37.9 + - + +
788M THR* 3.5 12.8 + - - +
789M ALA 3.1 0.2 - - - -
790M THR* 1.3 75.2 - - + +
792M ALA* 1.3 55.6 - - - +
794M CYS* 2.7 39.4 + - - +
795M ARG* 3.0 8.4 + - - +
111O LEU* 6.5 0.4 - - - -
114O LEU 2.5 25.1 + - - -
115O GLY* 2.6 8.7 - - - -
116O GLU* 2.4 69.2 + - + +
118O MET* 4.9 2.9 - - + -
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Residues in contact with ALA 792 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788M THR 3.2 1.9 + - - +
789M ALA 3.7 5.2 - - - +
791M GLN* 1.3 76.5 - - - +
793M ARG* 1.3 52.5 + - - +
795M ARG* 2.8 3.4 + - - -
796M GLY* 2.5 35.0 + - - -
35O ARG* 3.0 8.6 + - - +
40O ASN* 3.4 12.1 - - - +
42O THR* 2.3 63.0 - - + +
81O GLN* 4.8 1.8 - - - +
116O GLU* 4.0 1.0 + - - -
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Residues in contact with ARG 793 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789M ALA 3.8 10.5 + - - +
790M THR 4.4 4.0 - - - +
791M GLN 3.1 0.6 + - - -
792M ALA* 1.3 73.4 - - - +
794M CYS* 1.3 59.3 - - - +
796M GLY* 2.9 1.9 + - - -
797M PHE* 2.4 42.9 + - + +
800M ARG* 4.4 9.5 - - - +
40O ASN* 1.7 64.9 - - + +
79O LYS* 5.7 5.3 + - - +
82O GLY* 4.3 28.6 + - - -
87O PHE* 4.3 24.3 - - + -
146O ILE* 5.5 9.0 - - + -
147O MET* 4.3 29.7 - - + +
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Residues in contact with CYS 794 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790M THR* 2.7 36.6 - - - -
791M GLN* 2.7 17.2 + - - +
793M ARG* 1.3 79.6 - - - +
795M ARG* 1.3 50.2 + - - +
797M PHE* 2.9 9.9 + - - +
798M LEU* 2.4 44.4 + - + +
111O LEU* 4.7 20.2 - - + -
118O MET* 4.5 7.6 - - + -
126O LEU* 6.0 1.1 - - + -
146O ILE* 5.6 5.2 - - - -
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Residues in contact with ARG 795 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791M GLN 3.0 8.1 + - - +
792M ALA 2.8 4.1 + - - +
794M CYS* 1.3 70.3 - - - +
796M GLY* 1.3 66.7 + - - +
798M LEU* 2.9 12.5 + - - +
799M MET* 3.1 9.0 + - - +
35O ARG* 2.1 50.9 + - - +
43O ASN* 1.2 96.6 - - - +
44O ALA* 4.6 0.4 - - - +
116O GLU* 2.0 72.4 + - - +
117O LYS 4.5 1.6 + - - +
118O MET* 2.4 46.3 - - + +
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Residues in contact with GLY 796 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792M ALA 2.5 15.7 + - - -
793M ARG 3.2 3.1 - - - -
795M ARG* 1.3 77.5 - - - +
797M PHE* 1.3 52.6 + - - +
798M LEU 2.8 0.3 + - - -
799M MET* 2.7 22.0 + - - +
800M ARG* 3.1 13.1 + - - -
35O ARG* 2.6 37.5 - - - +
40O ASN* 3.8 8.1 - - - -
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Residues in contact with PHE 797 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793M ARG* 2.4 22.9 + - - +
794M CYS* 3.0 7.2 - - - +
796M GLY* 1.3 70.8 - - - -
798M LEU* 1.3 76.9 + - + +
800M ARG* 3.2 31.2 + - - +
801M VAL* 3.4 20.5 + - + +
126O LEU* 2.7 24.9 - - + -
145O HIS 3.8 3.4 - - - -
146O ILE* 2.4 83.7 - - + -
149O VAL* 2.7 29.6 - - + -
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Residues in contact with LEU 798 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794M CYS* 2.4 23.8 + - + +
795M ARG* 3.3 11.4 - - - +
796M GLY 2.8 0.6 + - - -
797M PHE* 1.3 87.9 - - + +
799M MET* 1.3 63.8 + - + +
801M VAL* 3.4 11.6 + - - +
802M GLU* 3.7 9.9 + - - +
111O LEU* 5.1 0.9 - - + -
118O MET* 4.7 20.0 - - + -
122O GLU* 3.4 42.1 - - + +
125O GLU* 6.4 0.2 - - + -
126O LEU* 2.1 72.0 - - + +
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Residues in contact with MET 799 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795M ARG 3.1 7.3 + - - +
796M GLY 2.7 11.4 + - - +
798M LEU* 1.3 72.1 - - + +
800M ARG* 1.3 59.1 + - - +
801M VAL 2.9 5.2 - - - -
802M GLU* 2.8 38.1 + - + +
803M TYR* 3.0 12.6 + - - +
806M MET* 5.6 8.3 - - - -
32O ASP* 2.3 69.3 - - + +
35O ARG* 4.8 4.5 - - + +
36O ALA* 6.0 1.7 - - - +
122O GLU* 5.3 7.9 - - - +
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Residues in contact with ARG 800 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793M ARG* 4.4 5.7 - - - +
796M GLY 3.1 6.8 + - - +
797M PHE* 3.2 39.6 + - - +
799M MET* 1.3 78.2 - - - +
801M VAL* 1.3 58.4 + - - +
803M TYR* 3.8 7.3 + - + +
804M ARG* 3.8 14.6 + - - +
35O ARG* 3.0 32.8 + - - +
36O ALA* 4.4 9.0 - - - +
38O GLY* 4.7 8.4 - - - -
39O GLN 4.1 5.0 + - - +
40O ASN* 1.4 49.2 + - - +
146O ILE 5.0 0.6 + - - -
147O MET* 6.2 0.2 - - - +
149O VAL* 3.4 54.6 + - + +
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Residues in contact with VAL 801 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797M PHE* 3.4 42.2 - - + +
798M LEU 3.4 7.2 + - - +
799M MET 2.9 1.0 - - - -
800M ARG* 1.3 77.2 - - - +
802M GLU* 1.3 73.7 + - - +
803M TYR 3.3 0.9 - - - -
804M ARG* 3.4 12.3 + - + +
805M ALA* 3.3 18.9 + - + +
808M GLU* 6.1 0.9 - - - +
125O GLU* 5.6 8.1 - - + +
126O LEU* 4.5 5.6 - - + -
149O VAL* 4.3 8.3 - - + -
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Residues in contact with GLU 802 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798M LEU 3.7 5.5 + - - +
799M MET* 2.8 32.4 + - + +
801M VAL* 1.3 87.4 - - - +
803M TYR* 1.3 65.3 + - - +
805M ALA* 3.2 10.8 + - - +
806M MET* 2.8 34.3 + - + +
809M ARG* 3.4 35.2 + - - -
122O GLU* 6.4 2.0 - - + -
125O GLU* 4.9 17.5 - - - +
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Residues in contact with TYR 803 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799M MET 3.0 11.5 + - - +
800M ARG* 4.2 7.6 - - - +
801M VAL 3.3 0.4 - - - -
802M GLU* 1.3 77.2 - - - +
804M ARG* 1.3 47.3 - - - +
805M ALA 3.1 0.2 - - - -
806M MET* 3.4 13.7 - - + +
807M VAL* 2.2 73.4 + - + +
13O ALA* 5.2 3.2 - - + +
16O LEU* 3.5 31.8 - - + +
17O PHE* 2.8 50.7 - + - -
36O ALA* 4.6 12.3 - - + -
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Residues in contact with ARG 804 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800M ARG 3.8 6.0 + - - +
801M VAL* 3.4 19.5 + - + +
802M GLU 3.3 0.6 - - - -
803M TYR* 1.3 76.7 - - - +
805M ALA* 1.3 52.0 + - - +
807M VAL* 3.5 12.0 - - + +
808M GLU* 2.5 45.9 + - + +
148O SER* 4.3 6.7 + - - -
149O VAL* 4.1 40.9 - - - +
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Residues in contact with ALA 805 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801M VAL* 3.3 10.5 + - + +
802M GLU* 3.2 21.9 + - - +
803M TYR 3.1 0.6 - - - -
804M ARG* 1.3 78.0 - - - +
806M MET* 1.3 50.5 + - - +
807M VAL 2.6 4.0 - - - -
808M GLU* 2.4 21.3 + - + +
809M ARG* 2.1 55.6 + - + +
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Residues in contact with MET 806 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799M MET* 5.6 7.6 - - - -
802M GLU* 2.8 33.8 + - + +
803M TYR* 3.4 23.6 - - + +
805M ALA* 1.3 71.2 - - - +
807M VAL* 1.8 46.4 - - + +
809M ARG* 2.9 30.4 - - - +
810M ARG* 2.6 33.2 + - - +
813M ILE* 5.3 1.9 - - - +
17O PHE* 5.2 10.1 - - + -
19O ARG* 5.5 9.2 - - - +
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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