Contacts of the helix formed by residues 977 - 988 (chain B) in PDB entry 2X2M
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 SER 977 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848B MET* 5.5 10.6 - - - +
972B ARG* 3.4 5.7 + - - +
975B ASN 4.3 0.2 - - - -
976B CYS* 1.3 83.0 - - - +
978B GLU* 1.3 63.7 + - - +
979B GLU* 3.6 6.6 + - - +
980B MET* 2.8 37.4 + - - +
981B TYR* 3.4 13.5 + - - +
1008B MET* 4.8 4.3 - - - -
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Residues in contact with GLU 978 (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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972B ARG* 3.0 23.6 - - - +
977B SER* 1.3 73.6 - - - +
979B GLU* 1.3 57.8 + - - +
981B TYR* 3.4 4.9 + - - +
982B ARG* 2.9 29.6 + - - +
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Residues in contact with GLU 979 (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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977B SER* 3.2 7.0 + - - +
978B GLU* 1.3 77.0 - - - +
980B MET* 1.3 64.0 + - - +
982B ARG* 3.3 8.6 + - - +
983B LEU* 3.0 22.9 + - - +
1008B MET* 4.2 20.4 - - + +
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Residues in contact with MET 980 (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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848B MET* 4.9 8.7 - - - -
851B LEU* 5.6 1.3 - - + -
852B ILE* 3.6 34.5 - - + +
855B ALA* 5.5 0.2 - - + -
941B LEU* 3.7 34.3 - - + -
944B ILE* 6.2 1.3 - - + -
945B VAL* 3.9 20.9 - - + -
976B CYS* 3.7 20.4 - - - -
977B SER* 2.8 22.0 + - - +
979B GLU* 1.3 74.9 - - - +
981B TYR* 1.3 62.7 + - - +
983B LEU* 2.9 24.5 + - - +
984B MET* 3.1 12.4 + - + +
1005B LEU* 4.3 5.2 - - + -
1008B MET* 4.1 18.5 - - - +
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Residues in contact with TYR 981 (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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969B ARG 5.0 0.7 + - - -
970B MET 2.7 29.0 + - - -
971B GLU* 3.7 5.0 - - - -
972B ARG* 3.4 51.6 + - + +
973B PRO* 4.3 1.6 - - + -
976B CYS* 3.7 5.8 - - - -
977B SER 3.4 15.3 + - - +
978B GLU* 3.8 4.0 - - - +
980B MET* 1.3 78.5 - - - +
982B ARG* 1.3 65.6 + - - +
984B MET* 2.8 38.1 + - - +
985B LEU* 3.0 50.4 + - + +
988B TRP* 4.5 4.9 - + - -
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Residues in contact with ARG 982 (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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978B GLU 2.9 19.5 + - - +
979B GLU* 3.4 10.1 - - - +
981B TYR* 1.3 75.8 - - - +
983B LEU* 1.3 57.1 + - - +
985B LEU* 3.6 10.9 + - - +
986B GLN* 3.1 28.4 + - - +
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Residues in contact with LEU 983 (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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941B LEU* 3.8 23.1 - - + -
979B GLU 3.0 11.8 + - - +
980B MET* 2.9 12.5 + - - +
982B ARG* 1.3 74.5 - - - +
984B MET* 1.3 62.4 + - - +
986B GLN* 3.4 4.7 + - + +
987B CYS* 3.1 29.7 + - - -
996B PRO* 4.5 10.1 - - + -
1001B ILE* 4.2 26.0 - - + -
1004B ASP* 3.9 24.0 - - + +
1005B LEU* 4.1 20.2 - - + -
1008B MET* 3.5 25.4 - - + -
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Residues in contact with MET 984 (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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938B GLY* 4.0 3.6 - - - +
941B LEU* 3.9 23.3 - - + -
942B TRP* 3.8 32.1 - - - +
945B VAL* 4.0 15.7 - - + -
973B PRO* 4.4 6.5 - - + -
976B CYS* 3.8 28.0 - - - -
980B MET* 3.1 13.1 + - + +
981B TYR* 2.8 28.5 + - + +
983B LEU* 1.3 68.2 - - - +
985B LEU* 1.3 65.3 + - - +
987B CYS* 3.0 18.9 + - - +
988B TRP* 3.0 44.7 + - + -
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Residues in contact with LEU 985 (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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969B ARG* 4.0 28.0 - - + -
981B TYR* 3.0 58.1 + - + +
982B ARG* 4.0 9.9 - - - +
984B MET* 1.3 76.0 - - - +
986B GLN* 1.3 55.6 + - - +
988B TRP* 2.7 30.6 + - + +
989B LYS* 3.1 14.6 + - + +
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Residues in contact with GLN 986 (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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982B ARG 3.1 16.8 + - - +
983B LEU* 3.8 7.4 - - + +
985B LEU* 1.3 77.0 - - - +
987B CYS* 1.3 61.5 + - - +
988B TRP 3.3 0.3 + - - -
989B LYS* 3.4 20.8 - - + +
994B LYS 4.3 10.1 - - - +
995B ARG* 3.3 17.3 - - - +
996B PRO* 3.3 28.4 - - + +
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Residues in contact with CYS 987 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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934B VAL* 3.6 40.2 - - - +
935B TRP* 3.5 12.0 - - - -
937B PHE* 4.7 5.6 - - - -
938B GLY* 3.6 21.1 - - - -
941B LEU* 4.8 1.1 - - - -
983B LEU* 3.1 29.9 + - - -
984B MET 3.0 12.5 + - - +
986B GLN* 1.3 75.9 - - - +
988B TRP* 1.3 58.7 + - + +
995B ARG* 3.2 23.6 + - - -
996B PRO* 4.3 8.5 - - - -
1001B ILE* 4.5 6.1 - - - -
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Residues in contact with TRP 988 (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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935B TRP* 3.1 54.0 + + + -
938B GLY* 3.4 21.7 - - - -
939B VAL* 3.4 16.6 - - + +
942B TRP* 4.3 3.1 - + + -
952B TYR* 5.1 4.0 - - - -
969B ARG* 2.9 51.9 + - + +
970B MET* 3.7 56.5 - - + -
981B TYR* 4.5 6.1 - + - -
984B MET* 3.0 41.4 + - + -
985B LEU* 2.7 22.5 + - + +
987B CYS* 1.3 75.6 - - + +
989B LYS* 1.3 65.9 + - - +
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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
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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