Contacts of the helix formed by residues 991 - 1006 (chain A) in PDB entry 4QMH
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 991 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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951A GLY* 3.6 17.1 + - - -
989A GLY 3.7 1.8 + - - -
990A GLY* 1.3 75.5 - - - +
992A PRO* 1.3 75.5 - - - +
993A ALA* 3.6 3.7 + - - -
994A LEU* 3.1 23.8 + - - +
995A LYS* 2.9 21.0 + - - +
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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 GLY 4.4 1.6 - - - +
991A SER* 1.3 88.1 - - - +
993A ALA* 1.3 57.2 + - - +
995A LYS* 3.4 16.0 + - - +
996A THR* 2.8 34.8 + - - -
1033A ARG* 5.3 11.7 - - - +
1034A ASN* 3.8 28.7 - - + +
1037A VAL* 3.7 3.6 - - + +
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Residues in contact with ALA 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 3.8 2.2 - - - -
951A GLY* 3.8 23.8 - - - +
952A ASP 4.2 9.0 - - - +
953A ASN* 5.8 1.6 - - - +
958A ARG* 4.3 14.4 - - - +
991A SER* 3.2 2.8 + - - +
992A PRO* 1.3 78.6 - - - +
994A LEU* 1.3 62.8 + - - +
996A THR* 3.3 6.9 + - - -
997A GLU* 3.0 27.5 + - - +
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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 LEU 3.3 31.0 - - - +
948A HIS* 4.3 14.6 - - + +
950A LEU* 3.7 12.7 - - + +
951A GLY* 3.7 10.0 - - - +
986A ALA* 3.3 41.1 - - + +
987A LEU* 4.3 2.5 - - - +
990A GLY* 4.3 7.4 - - - -
991A SER* 3.1 20.6 + - - +
993A ALA* 1.3 78.3 - - - +
995A LYS* 1.3 62.1 + - - +
997A GLU* 3.2 1.7 + - - +
998A LEU* 2.8 49.5 + - + +
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Residues in contact with LYS 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* 4.0 17.3 - - + +
990A GLY* 3.7 25.1 + - - +
991A SER 2.9 16.9 + - - +
992A PRO* 4.0 8.7 - - - +
994A LEU* 1.3 80.8 - - + +
996A THR* 1.3 63.6 + - - +
999A TRP* 3.0 37.4 + - + +
1029A HIS* 3.3 32.6 + - + +
1032A ASP* 2.8 29.8 + - - -
1033A ARG* 4.5 15.8 - - - +
1037A VAL* 3.9 24.5 - - + -
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Residues in contact with THR 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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992A PRO* 2.8 23.6 + - - +
993A ALA* 3.5 7.7 - - - -
994A LEU 3.2 0.2 - - - -
995A LYS* 1.3 76.1 - - - +
997A GLU* 1.3 68.3 + - - +
1000A ALA* 3.2 10.7 + - - +
1034A ASN* 4.3 1.2 + - - -
1036A ASP* 3.6 27.4 + - + +
1037A VAL* 3.6 17.5 - - - +
1040A ASN* 2.8 40.6 + - - +
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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* 3.6 34.5 - - + +
958A ARG* 3.0 38.0 + - + +
962A LEU* 3.4 25.8 - - + +
993A ALA 3.0 20.0 + - - +
994A LEU 3.9 2.7 - - - +
996A THR* 1.3 81.6 - - - +
998A LEU* 1.3 58.5 + - - +
1000A ALA* 3.3 8.1 + - - +
1001A TRP* 3.0 28.8 + - - +
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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 LEU* 3.8 27.1 - - + -
950A LEU* 4.3 9.4 - - + -
983A ILE* 3.9 17.5 - - + +
986A ALA* 3.9 24.2 - - + -
987A LEU* 3.8 32.5 - - + -
994A LEU* 2.8 29.2 + - + +
997A GLU* 1.3 70.3 - - - +
999A TRP* 1.3 60.9 + - - +
1001A TRP* 3.2 23.9 + - + -
1002A LEU* 2.9 38.1 + - + +
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Residues in contact with TRP 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* 3.7 30.2 - - + +
995A LYS* 3.0 30.2 + - + +
998A LEU* 1.3 73.0 - - - +
1000A ALA* 1.3 60.9 + - - +
1002A LEU* 3.7 22.2 - - + +
1003A ALA* 2.9 30.7 + - - +
1022A MET* 4.0 8.7 - - + -
1025A HIS 3.7 4.9 - - - -
1026A LEU* 3.5 52.7 - - + -
1029A HIS* 2.9 28.6 + - + +
1037A VAL* 4.5 4.5 - - + -
1040A ASN* 3.7 22.4 - - + +
1041A ALA* 3.8 18.6 - - + -
1044A ALA* 3.5 24.9 - - + +
1048A ILE* 4.5 10.5 - - + -
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Residues in contact with ALA1000 (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 THR 3.2 20.1 + - - +
997A GLU* 3.5 8.7 - - - +
999A TRP* 1.3 77.1 - - - +
1001A TRP* 1.3 57.6 + - - +
1003A ALA* 3.3 5.9 + - - +
1004A ASP* 2.9 31.2 + - - +
1040A ASN* 3.7 17.6 - - - +
1043A GLU* 5.9 1.8 - - - -
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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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943A PHE* 4.5 3.8 - + - -
947A LEU* 5.8 0.4 - - + -
950A LEU* 5.8 0.9 - - + -
962A LEU* 4.1 24.9 - - + -
965A ILE* 3.6 28.2 - - + +
966A ASN* 2.9 29.2 + - - -
974A TYR* 3.8 20.4 - + - -
977A PHE* 3.8 20.6 - + + -
978A PHE* 4.0 15.9 - + - -
983A ILE* 3.8 15.0 - - + -
997A GLU 3.0 16.6 + - - +
998A LEU* 3.6 19.5 - - + +
999A TRP 3.2 0.2 - - - -
1000A ALA* 1.3 75.1 - - - +
1002A LEU* 1.3 94.0 + - + +
1004A ASP* 3.2 5.1 + - - +
1005A LYS* 2.9 52.2 + - + +
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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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978A PHE* 3.8 22.0 - - + -
983A ILE* 3.9 25.1 - - + -
987A LEU* 4.4 5.6 - - + -
998A LEU* 2.9 24.3 + - + +
999A TRP* 3.7 34.1 - - + +
1001A TRP* 1.3 100.6 - - + +
1003A ALA* 1.3 63.4 + - - +
1005A LYS* 4.5 0.9 - - - +
1006A LEU* 3.0 48.7 + - + +
1022A MET* 4.1 11.0 - - - -
1044A ALA* 4.7 2.7 - - + -
1047A GLY* 5.2 0.2 - - - -
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Residues in contact with ALA1003 (chain A).
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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999A TRP 2.9 19.2 + - - +
1000A ALA* 3.7 7.2 - - - +
1002A LEU* 1.3 76.0 - - - +
1004A ASP* 1.3 57.9 + - - +
1007A PRO* 3.1 25.3 - - - +
1043A GLU* 3.6 37.5 - - + +
1044A ALA* 3.7 15.4 - - - +
1047A GLY* 5.6 2.0 + - - -
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Residues in contact with ASP1004 (chain A).
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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1000A ALA 2.9 17.8 + - - +
1001A TRP* 3.6 8.0 - - - +
1002A LEU 3.2 0.2 - - - -
1003A ALA* 1.3 79.7 - - - +
1005A LYS* 1.3 83.2 + - + +
1007A PRO* 3.9 5.4 - - - +
1008A GLY* 4.8 2.4 + - - -
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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 31.7 + - - +
970A GLU* 4.2 7.9 + - - -
974A TYR* 3.2 26.9 + - + +
978A PHE* 5.7 0.7 - - + -
1001A TRP* 2.9 47.8 + - + +
1002A LEU* 4.6 1.3 - - - +
1004A ASP* 1.3 95.9 + - - +
1006A LEU* 1.3 66.9 + - + +
1007A PRO* 3.3 2.2 - - - -
1008A GLY* 3.1 13.3 + - - -
1009A LEU* 3.4 26.2 + - + +
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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 PHE* 3.8 30.3 - - + -
1002A LEU* 3.0 38.4 + - + +
1005A LYS* 1.3 77.2 - - - +
1007A PRO* 1.3 67.6 - - + +
1008A GLY 3.1 0.9 + - - -
1009A LEU* 3.2 11.6 + - + +
1014A VAL* 4.4 4.5 - - + -
1019A ILE* 3.9 15.5 - - + -
1044A ALA 5.2 0.7 - - - +
1047A GLY* 3.8 21.8 - - - +
1048A ILE* 3.7 31.4 - - + +
1050A ILE* 4.7 0.2 - - - +
1051A HIS* 2.8 36.8 + - + +
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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