Contacts of the helix formed by residues 991 - 1006 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A GLY* 3.1 28.2 + - - -
989A LYS* 2.9 12.6 + - + +
990A GLU* 1.3 73.7 - - - +
992A PRO* 1.3 62.1 - - - +
993A PHE* 2.9 27.5 + - - +
994A LEU* 3.0 24.8 + - + +
995A ARG* 3.0 30.3 + - - +
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Residues in contact with PRO 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990A GLU 3.8 8.1 - - - +
991A ASN* 1.3 84.9 - - - +
993A PHE* 1.3 82.2 + - + +
995A ARG* 4.5 2.0 - - + -
996A GLN* 3.1 27.9 + - - +
1029A ASP* 4.6 4.5 - - - +
1031A ASN* 3.8 35.7 - - + +
1034A VAL* 3.3 12.7 - - + +
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Residues in contact with PHE 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950A LEU 3.5 5.2 - - - +
951A GLY 4.0 10.3 - - - +
952A ASP 3.9 6.5 - - - +
953A SER* 3.8 27.8 - - - -
955A ASN* 5.1 0.9 - - - -
958A ARG* 3.4 46.2 - - - +
991A ASN* 2.9 13.7 + - - +
992A PRO* 1.3 90.1 - - + +
994A LEU* 1.3 64.9 + - - +
996A GLN* 3.5 13.0 - - - +
997A GLU* 3.2 30.5 + - - +
1031A ASN* 6.2 1.8 - - - -
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Residues in contact with LEU 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ILE* 3.3 37.9 - - + +
948A THR* 4.7 9.9 - - - +
950A LEU* 3.6 15.2 + - + -
951A GLY* 3.8 10.5 - - - +
986A GLU* 3.6 40.6 - - + +
987A LEU* 5.5 0.4 - - - -
989A LYS* 4.1 17.0 - - + -
991A ASN* 3.0 20.8 + - + +
993A PHE* 1.3 77.1 - - - +
995A ARG* 1.3 64.6 + - + +
997A GLU* 4.0 0.5 - - - +
998A LEU* 3.0 37.1 + - + +
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Residues in contact with ARG 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A LEU* 3.2 25.7 + - + +
988A LYS* 3.3 23.6 + - - +
989A LYS 3.0 21.4 + - - +
990A GLU* 4.0 18.4 - - - +
991A ASN 3.0 21.5 + - - +
992A PRO* 4.9 0.4 - - - -
994A LEU* 1.3 76.5 - - + +
996A GLN* 1.3 57.9 + - - +
998A LEU* 4.0 0.2 - - - +
999A LEU* 2.9 37.9 + - - +
1022A HIS* 4.9 2.8 + - - +
1025A SER* 3.9 27.7 + - - -
1026A CYS* 3.6 30.7 - - - +
1029A ASP* 2.7 38.1 + - - +
1034A VAL* 4.0 11.4 - - + -
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Residues in contact with GLN 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A ARG* 5.6 6.4 - - - +
992A PRO 3.1 23.8 + - - +
993A PHE* 3.5 16.0 - - - +
995A ARG* 1.3 78.7 - - - +
997A GLU* 1.3 66.9 + - + +
999A LEU* 4.0 0.2 - - - +
1000A GLY* 3.1 23.0 + - - -
1031A ASN* 3.8 14.6 + - - +
1033A ASP* 3.6 44.0 + - + +
1034A VAL* 3.9 7.3 - - + +
1037A LYS* 3.7 30.3 + - + +
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Residues in contact with GLU 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950A LEU* 3.9 35.9 - - + +
958A ARG* 3.5 32.0 + - - +
959A ALA* 5.8 1.0 - - - -
962A LEU* 3.9 27.3 - - + +
993A PHE 3.2 18.0 + - - +
994A LEU 4.0 2.5 - - - +
996A GLN* 1.3 87.8 + - + +
998A LEU* 1.3 61.8 + - - +
1000A GLY* 3.3 2.4 + - - -
1001A TRP* 2.9 28.5 + - - +
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Residues in contact with LEU 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ILE* 4.2 15.3 - - + -
950A LEU* 4.2 5.8 - - + +
983A LEU* 3.7 38.8 - - + +
986A GLU* 4.2 7.9 - - + -
987A LEU* 3.9 41.5 - - + +
994A LEU* 3.0 23.7 + - + +
995A ARG 4.0 2.0 - - - +
997A GLU* 1.3 79.7 - - - +
999A LEU* 1.3 56.8 + - - +
1001A TRP* 3.2 25.6 + - + +
1002A LEU* 2.9 38.3 + - + +
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Residues in contact with LEU 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A LEU* 4.2 23.1 - - + -
995A ARG 2.9 22.4 + - - +
998A LEU* 1.3 75.0 - - - +
1000A GLY* 1.3 64.9 + - - +
1002A LEU* 3.4 10.9 + - + +
1003A ALA* 3.0 23.9 + - - +
1023A LEU* 3.7 28.0 - - + -
1026A CYS* 3.7 31.0 - - + -
1034A VAL* 3.7 22.7 - - + +
1037A LYS* 3.7 19.2 - - + +
1038A ALA* 3.7 8.3 - - + +
1041A ALA* 4.1 10.1 - - + +
1045A PHE* 5.2 0.2 - - + -
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Residues in contact with GLY1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996A GLN 3.1 15.5 + - - -
997A GLU* 3.7 4.0 - - - -
998A LEU 3.3 0.2 - - - -
999A LEU* 1.3 77.1 - - - +
1001A TRP* 1.3 62.1 + - - +
1003A ALA* 3.3 6.3 + - - +
1004A GLU* 3.2 24.1 + - - +
1037A LYS* 4.2 20.3 - - - +
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Residues in contact with TRP1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ILE* 3.8 21.3 - - + -
950A LEU* 5.6 1.8 - - + -
962A LEU* 4.0 20.4 - - + +
965A VAL* 3.7 39.2 - - + +
966A ASN* 2.7 29.1 + - - -
969A ALA* 4.3 2.7 - - + -
974A MET* 3.6 35.7 - - + -
977A TRP* 4.0 23.8 - + + -
983A LEU* 4.8 8.7 - - + -
997A GLU 2.9 17.0 + - - +
998A LEU* 3.5 23.8 - - + +
1000A GLY* 1.3 77.0 - - - +
1002A LEU* 1.3 59.4 + - + +
1004A GLU* 3.3 12.1 + - - +
1005A LYS* 2.9 46.8 + - + +
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Residues in contact with LEU1002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974A MET* 5.4 4.5 - - + -
978A LEU* 3.9 28.5 - - + -
983A LEU* 4.3 11.2 - - + -
987A LEU* 4.7 11.2 - - + -
998A LEU* 2.9 30.4 + - + +
999A LEU* 3.7 15.3 - - + +
1001A TRP* 1.3 79.1 - - + +
1003A ALA* 1.3 57.0 + - - +
1005A LYS* 4.8 1.8 - - + -
1006A LEU* 2.9 58.9 + - + +
1016A LEU* 5.0 5.2 - - + -
1019A CYS* 4.9 7.6 - - - -
1041A ALA* 5.0 0.9 - - + -
1045A PHE* 3.9 28.0 - - + -
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Residues in contact with ALA1003 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999A LEU 3.0 17.2 + - - +
1000A GLY* 3.8 7.0 - - - +
1001A TRP 3.3 0.2 - - - -
1002A LEU* 1.3 76.4 - - - +
1004A GLU* 1.3 61.5 + - - +
1007A PRO* 3.4 17.2 - - - +
1037A LYS* 5.2 0.4 - - + +
1040A ASP* 4.3 11.0 - - + +
1041A ALA* 4.1 16.3 - - - +
1044A PHE* 3.8 35.7 - - + -
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Residues in contact with GLU1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962A LEU* 5.8 2.6 - - - +
966A ASN* 4.5 12.2 + - - +
1000A GLY 3.2 12.9 + - - +
1001A TRP* 3.6 20.6 - - - +
1002A LEU 3.2 0.2 - - - -
1003A ALA* 1.3 78.9 - - - +
1005A LYS* 1.3 73.8 + - + +
1007A PRO* 3.4 12.3 - - - +
1008A THR* 3.8 12.1 - - - +
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Residues in contact with LYS1005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A ASN* 3.2 30.0 + - - +
969A ALA* 4.4 13.2 - - - +
970A GLU* 5.6 3.4 - - - +
974A MET* 3.8 42.1 - - + +
1001A TRP* 2.9 35.9 + - + +
1002A LEU* 4.4 2.2 - - + +
1004A GLU* 1.3 89.7 + - + +
1006A LEU* 1.3 65.5 + - + +
1007A PRO* 3.3 3.4 - - - -
1008A THR* 2.9 30.8 + - + +
1009A LEU* 3.4 10.7 - - + +
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Residues in contact with LEU1006 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978A LEU* 4.3 10.3 - - + -
1002A LEU* 2.9 35.5 + - + +
1003A ALA* 5.2 0.2 - - - -
1005A LYS* 1.3 77.4 - - + +
1007A PRO* 1.3 64.4 - - + +
1008A THR 3.3 0.9 + - - -
1009A LEU* 3.5 28.3 + - + +
1016A LEU* 4.1 27.4 - - + -
1041A ALA 4.8 0.4 - - - +
1044A PHE* 3.6 39.0 - - + +
1045A PHE* 3.8 28.3 - - + -
1047A MET* 4.2 0.9 - - - -
1048A HIS* 2.8 27.8 + - + +
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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