Contacts of the helix formed by residues 991 - 1006 (chain B) in PDB entry 4QMI
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 ASN 991 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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951B GLY* 2.9 34.4 + - - -
989B LYS* 2.8 14.8 + - + +
990B GLU* 1.3 73.3 - - - +
992B PRO* 1.3 63.0 - - - +
993B PHE* 2.8 28.2 + - - +
994B LEU* 3.1 19.4 + - + +
995B ARG* 3.0 31.5 + - - +
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Residues in contact with PRO 992 (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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990B GLU 3.7 8.3 - - - +
991B ASN* 1.3 84.2 - - - +
993B PHE* 1.3 78.6 + - + +
995B ARG* 4.5 2.2 - - + -
996B GLN* 3.1 30.8 + - - +
1029B ASP* 4.5 6.1 - - - +
1031B ASN* 3.8 35.7 - - + +
1034B VAL* 3.3 11.6 - - + +
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Residues in contact with PHE 993 (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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950B LEU 3.4 14.1 - - - +
951B GLY* 4.0 10.5 - - - -
952B ASP 3.8 7.0 - - - +
953B SER* 3.8 28.7 - - - -
955B ASN* 5.2 0.7 - - - -
958B ARG* 3.3 37.2 - - - +
991B ASN* 2.8 12.8 + - - +
992B PRO* 1.3 87.9 - - + +
994B LEU* 1.3 65.7 + - - +
996B GLN* 3.5 13.4 - - - +
997B GLU* 3.1 29.6 + - - +
1031B ASN* 6.3 0.9 - - - -
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Residues in contact with LEU 994 (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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947B ILE* 3.9 22.0 - - + +
948B THR* 4.3 13.2 - - + +
950B LEU* 3.5 11.7 + - + +
951B GLY* 3.7 10.8 - - - +
986B GLU* 3.7 46.0 - - + +
987B LEU* 4.8 0.4 - - - -
989B LYS* 4.2 15.5 - - + +
991B ASN* 3.1 20.4 + - + +
993B PHE* 1.3 77.7 - - - +
995B ARG* 1.3 60.4 + - + +
997B GLU* 3.8 0.5 - - - +
998B LEU* 2.8 57.5 + - + +
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Residues in contact with ARG 995 (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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987B LEU* 3.2 26.1 + - + +
988B LYS* 3.3 23.0 + - - +
989B LYS 3.0 20.1 + - - +
990B GLU* 3.9 19.3 + - - +
991B ASN 3.0 21.1 + - - +
994B LEU* 1.3 76.6 - - + +
996B GLN* 1.3 57.8 + - - +
998B LEU* 4.2 0.2 - - - +
999B LEU* 3.0 39.3 + - - +
1022B HIS* 4.7 2.8 + - - +
1025B SER* 4.1 29.6 + - - -
1026B CYS* 3.5 26.5 - - - -
1029B ASP* 2.8 37.7 + - - +
1034B VAL* 3.9 17.3 - - + -
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Residues in contact with GLN 996 (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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958B ARG* 5.9 4.2 - - - +
992B PRO* 3.1 22.1 + - - +
993B PHE* 3.5 16.7 - - - +
995B ARG* 1.3 79.6 - - - +
997B GLU* 1.3 72.5 + - + +
1000B GLY* 3.0 19.2 + - - -
1031B ASN* 3.7 14.9 + - - +
1033B ASP* 3.5 46.9 + - + +
1034B VAL* 3.9 5.0 - - - +
1037B LYS* 3.6 27.5 - - + +
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Residues in contact with GLU 997 (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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950B LEU* 4.0 28.9 - - + +
958B ARG* 3.2 41.1 + - - +
962B LEU* 4.1 24.2 - - + +
993B PHE 3.1 18.6 + - - +
994B LEU 4.0 1.8 - - - +
996B GLN* 1.3 90.4 + - + +
998B LEU* 1.3 58.5 + - - +
1000B GLY* 3.3 2.2 + - - -
1001B TRP* 2.9 28.9 + - - +
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Residues in contact with LEU 998 (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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947B ILE* 3.9 19.5 - - + -
950B LEU* 4.3 7.6 - - + +
983B LEU* 3.9 37.7 - - + +
986B GLU* 4.2 0.2 - - + -
987B LEU* 3.8 41.1 - - + +
994B LEU* 2.8 33.8 + - + +
995B ARG 4.2 1.6 - - - +
997B GLU* 1.3 74.5 - - - +
999B LEU* 1.3 60.8 + - - +
1001B TRP* 3.3 16.8 + - + +
1002B LEU* 2.9 41.7 + - + +
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Residues in contact with LEU 999 (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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987B LEU* 4.0 24.9 - - + -
995B ARG 3.0 23.1 + - - +
998B LEU* 1.3 76.7 - - - +
1000B GLY* 1.3 62.4 + - - +
1002B LEU* 3.7 11.4 - - + +
1003B ALA* 3.0 24.1 + - - +
1023B LEU* 3.8 26.5 - - + -
1026B CYS* 3.8 29.4 - - + -
1034B VAL* 4.0 7.2 - - + +
1037B LYS* 3.8 18.1 - - + +
1038B ALA* 3.7 19.3 - - + +
1041B ALA* 4.1 14.9 - - + +
1045B PHE* 5.0 1.1 - - + -
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Residues in contact with GLY1000 (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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996B GLN 3.0 15.2 + - - -
997B GLU* 3.7 4.0 - - - -
999B LEU* 1.3 76.7 - - - +
1001B TRP* 1.3 62.0 + - - +
1003B ALA* 3.4 6.7 + - - +
1004B GLU* 3.3 22.8 + - - +
1037B LYS* 4.2 21.9 - - - +
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Residues in contact with TRP1001 (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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947B ILE* 3.9 20.2 - - + -
950B LEU* 5.6 1.6 - - + -
962B LEU* 3.8 24.6 - - + +
965B VAL* 3.9 31.7 - - + +
966B ASN* 2.8 30.1 + - - -
969B ALA* 4.0 5.2 - - + -
974B MET* 3.7 38.6 - - + -
977B TRP* 4.0 26.0 - + + -
983B LEU* 4.9 5.2 - - + -
997B GLU 2.9 17.2 + - - +
998B LEU* 3.5 24.0 - - + +
1000B GLY* 1.3 76.4 - - - +
1002B LEU* 1.3 61.1 + - + +
1004B GLU* 3.2 12.4 + - - +
1005B LYS* 2.9 43.1 + - + +
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Residues in contact with LEU1002 (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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974B MET* 4.7 11.0 - - + -
978B LEU* 4.0 26.9 - - + -
983B LEU* 4.1 13.2 - - + -
987B LEU* 4.9 7.4 - - + -
998B LEU* 2.9 35.4 + - + +
999B LEU* 3.7 13.7 - - + +
1000B GLY 3.3 0.2 - - - -
1001B TRP* 1.3 76.8 - - + +
1003B ALA* 1.3 60.6 + - - +
1005B LYS* 4.4 2.0 - - - +
1006B LEU* 2.9 55.1 + - + +
1016B LEU* 5.4 1.3 - - + -
1019B CYS* 5.1 5.6 - - - -
1041B ALA* 5.3 0.9 - - + -
1045B PHE* 4.1 26.9 - - + -
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Residues in contact with ALA1003 (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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999B LEU 3.0 17.4 + - - +
1000B GLY* 3.8 7.6 - - - +
1002B LEU* 1.3 77.6 - - - +
1004B GLU* 1.3 61.7 + - - +
1007B PRO* 3.4 14.0 - - - +
1037B LYS 5.6 0.2 - - - +
1040B ASP* 4.6 8.3 - - + +
1041B ALA* 4.3 12.9 - - + +
1044B PHE* 3.6 42.0 - - + -
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Residues in contact with GLU1004 (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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962B LEU* 6.2 0.2 - - - +
966B ASN* 4.0 23.5 + - - +
1000B GLY 3.3 11.1 + - - +
1001B TRP* 3.2 15.5 + - - +
1002B LEU 3.1 0.4 - - - -
1003B ALA* 1.3 80.3 - - - +
1005B LYS* 1.3 68.5 + - + +
1007B PRO* 3.5 10.1 - - - +
1008B THR* 4.1 8.8 - - - +
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Residues in contact with LYS1005 (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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966B ASN* 3.6 23.7 + - - -
969B ALA* 4.2 24.2 - - - +
970B GLU* 4.9 6.9 - - - +
974B MET* 3.8 36.9 - - + +
1001B TRP* 2.9 34.1 + - + +
1002B LEU* 3.3 1.8 + - - +
1004B GLU* 1.3 87.2 - - + +
1006B LEU* 1.3 60.4 + - - +
1007B PRO* 3.2 3.8 - - - -
1008B THR* 2.8 45.0 + - + +
1009B LEU* 3.4 6.9 - - - +
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Residues in contact with LEU1006 (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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974B MET* 6.1 0.2 - - + -
978B LEU* 3.8 16.4 - - + -
1002B LEU* 2.9 35.9 + - + +
1003B ALA* 5.3 0.2 - - - -
1005B LYS* 1.3 77.8 - - - +
1007B PRO* 1.4 66.1 - - + +
1008B THR 3.3 0.7 + - - -
1009B LEU* 3.6 32.8 + - + +
1016B LEU* 4.1 22.2 - - + -
1041B ALA* 6.0 0.2 - - + -
1044B PHE* 3.9 35.0 - - + +
1045B PHE* 4.0 24.7 - - + +
1047B MET* 3.9 4.9 - - + -
1048B HIS* 2.8 27.4 + - + +
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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