Contacts of the helix formed by residues 709 - 719 (chain B) in PDB entry 1M2V
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 MET 709 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B PRO* 5.0 4.3 - - - -
150B PRO* 5.0 2.5 - - - -
151B ILE* 3.3 37.7 - - + -
153B ASP* 3.6 28.7 - - + +
154B LEU* 3.2 43.5 - - + -
648B GLN* 3.0 28.3 + - - +
708B ARG* 1.3 83.0 - - - +
710B PHE* 1.3 60.1 + - - +
711B PRO 3.5 1.3 - - - -
712B LEU* 3.2 23.7 + - + +
713B LEU* 2.9 35.6 + - + +
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Residues in contact with PHE 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B GLN* 3.8 22.8 + - + +
651B ILE* 3.5 24.2 - - + -
652B ALA* 4.3 5.4 - - + -
655B TYR* 3.9 12.3 - + - -
678B SER* 3.7 17.0 - - - -
679B VAL* 3.8 18.2 - - + -
682B ILE* 3.5 36.3 - - + -
683B LEU* 6.3 0.4 - - + -
703B LEU* 5.6 1.6 - - + -
707B LEU* 3.0 22.2 + - + +
709B MET* 1.3 77.3 - - - +
711B PRO* 1.3 73.2 - - + +
713B LEU* 3.2 6.0 + - - +
714B MET* 3.0 54.0 + - + +
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Residues in contact with PRO 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.9 22.2 - - + -
679B VAL* 3.8 24.5 - - + -
683B LEU* 4.2 9.4 - - + -
703B LEU* 4.0 8.7 - - + -
707B LEU 3.2 13.7 - - - +
708B ARG 4.2 5.8 - - - +
709B MET 3.8 1.3 - - - -
710B PHE* 1.3 95.9 - - + +
712B LEU* 1.3 61.5 + - - +
714B MET* 4.1 0.5 - - - +
715B HIS* 3.1 25.5 + - - +
913B TYR* 4.2 12.1 - - - +
916B PHE* 3.4 6.3 - - + -
917B LEU* 4.5 13.2 - - + -
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Residues in contact with LEU 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 3.7 15.7 - - + -
151B ILE* 3.5 18.2 - - + -
708B ARG 4.9 1.3 - - - +
709B MET* 3.2 39.6 + - + +
711B PRO* 1.3 80.6 - - - +
713B LEU* 1.3 62.6 + - + +
715B HIS* 3.5 3.2 + - + +
716B SER* 2.9 36.2 + - - +
753B TYR* 3.8 21.5 - - + -
903B VAL 5.6 0.4 - - - +
904B GLU* 4.3 8.5 - - + -
913B TYR* 3.6 46.8 + - + +
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Residues in contact with LEU 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.1 13.9 - - + -
648B GLN 4.6 2.5 - - - +
649B LEU* 3.7 26.5 - - + -
652B ALA* 3.7 30.5 - - + -
709B MET* 2.9 25.1 + - + +
710B PHE* 3.7 3.8 - - - +
712B LEU* 1.3 74.6 - - + +
714B MET* 1.3 70.5 + - + +
716B SER* 3.1 3.5 + - - -
717B LEU* 3.0 19.1 + - - +
749B ILE* 4.0 25.4 - - + -
752B ILE* 3.4 22.4 - - + +
753B TYR* 4.2 21.8 - - + -
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Residues in contact with MET 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B ALA* 3.6 42.4 - - + +
655B TYR* 3.8 19.3 - - - -
675B ILE* 3.2 31.8 - - + +
678B SER* 3.9 4.3 - - - +
679B VAL* 3.3 23.1 - - + -
710B PHE* 3.0 43.9 + - + +
713B LEU* 1.3 79.4 - - + +
715B HIS* 1.3 61.3 + - - +
717B LEU* 3.0 32.4 + - + +
718B THR* 3.3 4.4 + - - +
752B ILE* 5.3 2.9 - - + -
916B PHE* 5.4 0.7 - - + -
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Residues in contact with HIS 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B ASN* 5.7 0.4 + - - -
711B PRO 3.1 18.6 + - - +
712B LEU* 3.7 5.2 - - + +
714B MET* 1.3 74.3 - - - +
716B SER* 1.3 67.2 + - - +
718B THR* 2.5 30.6 + - - -
719B LYS* 2.9 43.0 + - - +
903B VAL 3.8 14.6 - - - -
910B ASN* 4.0 10.1 - - - -
911B GLU* 3.7 12.2 + - + -
912B SER 4.0 1.6 - - - -
913B TYR* 3.8 24.4 + + + -
916B PHE* 3.4 47.9 - + + -
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Residues in contact with SER 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B LEU* 2.9 19.8 + - - +
713B LEU* 3.4 8.9 - - - -
715B HIS* 1.3 77.1 - - - +
717B LEU* 1.3 58.1 + - - +
719B LYS* 2.9 20.4 + - - +
720B HIS* 3.1 11.3 + - - +
752B ILE* 3.4 30.2 - - - +
753B TYR* 3.9 11.1 - - - -
903B VAL* 3.2 33.6 + - - +
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Residues in contact with LEU 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B ASN* 3.8 38.1 - - + +
675B ILE* 3.7 26.0 - - + -
713B LEU 3.0 11.6 + - - +
714B MET* 3.0 33.6 + - + +
716B SER* 1.3 76.7 - - - +
718B THR* 1.3 55.1 + - - +
720B HIS* 2.8 30.0 + - + +
723B PHE* 3.7 15.6 - - + +
740B LEU* 4.0 14.1 - - + -
752B ILE* 3.6 31.8 - - + +
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Residues in contact with THR 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B ARG* 4.3 19.2 - - + +
675B ILE* 4.0 21.8 - - + -
676B ASN* 3.9 23.0 + - - +
714B MET 3.8 10.3 - - - +
715B HIS* 2.5 31.5 + - - -
717B LEU* 1.3 75.9 - - - +
719B LYS* 1.3 58.0 + - - +
720B HIS 3.4 0.2 - - - -
723B PHE* 4.0 11.3 - - - +
724B ARG* 3.7 20.3 + - - -
910B ASN* 4.1 23.0 + - - -
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Residues in contact with LYS 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B HIS* 2.9 38.2 + - - +
716B SER 2.9 10.1 + - - +
718B THR* 1.3 78.1 - - - +
720B HIS* 1.3 65.5 + - - +
724B ARG* 3.2 25.4 + - - +
900B SER 5.1 1.0 - - - +
903B VAL* 3.0 43.3 + - + +
905B ASP 2.6 22.4 + - - -
907B ILE* 4.7 9.9 - - + +
908B LEU* 3.8 10.9 - - + +
910B ASN* 3.9 22.9 - - + +
911B GLU 2.6 27.9 + - - -
912B SER* 3.8 1.8 - - - +
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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