Contacts of the helix formed by residues 991 - 1011 (chain A) in PDB entry 4C3I
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 LYS 991 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977A MET* 3.8 24.3 - - + +
983A LYS* 5.3 7.5 - - - +
989A GLY 4.4 0.2 + - - -
990A ILE* 1.4 72.4 - - - +
992A PRO* 1.4 70.9 - - + +
993A GLN* 4.0 8.7 - - - +
994A GLU* 3.0 29.1 + - + +
995A TYR* 2.8 25.3 + - - +
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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 ILE 4.7 0.4 - - - +
991A LYS* 1.4 85.6 - - + +
993A GLN* 1.3 69.8 + - + +
995A TYR* 3.3 10.7 + - + +
996A TYR* 3.0 25.3 + - - +
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Residues in contact with GLN 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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966A LEU* 3.9 16.3 - - + +
968A SER* 3.2 27.3 + - - +
969A PHE* 3.7 38.8 - - + -
977A MET* 3.8 15.8 - - + +
991A LYS* 4.0 8.3 - - - +
992A PRO* 1.3 90.7 - - + +
994A GLU* 1.4 60.7 + - - +
996A TYR* 3.5 3.5 + - - +
997A PHE* 3.1 31.9 + - + -
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Residues in contact with GLU 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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977A MET* 3.9 25.5 - - + +
981A TYR 4.3 2.1 - - - +
982A VAL* 3.5 39.2 - - + +
983A LYS* 3.1 30.5 + - - +
984A GLY* 3.5 8.9 + - - -
989A GLY 4.8 0.2 - - - +
990A ILE* 3.7 11.5 - - + -
991A LYS* 3.0 39.5 + - + +
993A GLN* 1.4 70.6 - - - +
995A TYR* 1.4 54.9 + - - +
997A PHE* 3.4 7.7 + - + +
998A HIS* 2.8 35.8 + - - +
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Residues in contact with TYR 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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990A ILE* 3.7 31.8 - - + +
991A LYS 2.8 15.4 + - - +
992A PRO* 3.3 16.4 - - + +
994A GLU* 1.4 72.4 - - - +
996A TYR* 1.3 60.6 + + + +
998A HIS* 3.4 3.3 + - - +
999A CYS* 2.9 51.0 + - - -
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Residues in contact with TYR 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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966A LEU* 3.7 31.6 - - + -
992A PRO 3.0 15.9 + - - +
993A GLN 3.7 5.2 - - - +
995A TYR* 1.3 77.9 - + + +
997A PHE* 1.3 58.3 + + - +
999A CYS* 3.3 10.7 + - + +
1000A MET* 3.1 56.4 + - + +
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Residues in contact with PHE 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 GLN* 4.0 15.9 - - + +
952A LEU* 4.6 1.4 - - - +
957A VAL* 3.5 34.3 - - + -
965A THR* 3.8 5.8 - - - -
966A LEU* 3.5 27.8 - - + -
969A PHE* 3.7 24.9 - + - -
977A MET* 3.3 23.1 - - + -
978A ALA 3.6 18.4 - - - -
980A GLY* 3.6 17.0 - - - +
982A VAL* 5.7 0.2 - - + -
993A GLN 3.1 19.5 + - - +
994A GLU* 3.7 9.6 - - + +
995A TYR 3.3 0.2 - - - -
996A TYR* 1.3 73.1 - - - +
998A HIS* 1.3 63.9 + - - +
1000A MET* 3.3 18.8 - - + +
1001A ALA* 3.3 21.3 + - - +
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Residues in contact with HIS 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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942A GLN* 5.3 4.9 - - - -
947A LEU* 3.7 23.1 - - + -
950A GLN* 3.1 25.8 + - - +
986A PHE* 3.5 25.1 - + - -
990A ILE* 4.0 17.9 - - + -
994A GLU 2.8 17.7 + - - +
995A TYR 3.6 5.4 - - - +
996A TYR 3.3 0.2 - - - -
997A PHE* 1.3 73.0 - - - +
999A CYS* 1.3 55.6 + - - +
1001A ALA* 3.4 0.7 + - - +
1002A GLY* 2.8 39.6 + - - -
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Residues in contact with CYS 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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995A TYR* 2.9 41.7 + - - +
996A TYR* 3.4 17.3 - - + +
998A HIS* 1.3 77.8 - - - +
1000A MET* 1.3 60.1 + - - +
1002A GLY* 5.1 0.7 - - - -
1003A ARG* 3.1 30.9 + - - +
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Residues in contact with MET1000 (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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952A LEU* 3.6 20.4 - - + +
957A VAL* 4.4 2.0 - - + -
958A PRO* 3.8 35.9 - - + +
965A THR 5.1 4.9 - - - +
966A LEU* 5.2 0.4 - - + -
996A TYR* 3.1 43.8 + - + +
997A PHE* 3.3 32.5 - - + +
998A HIS 3.3 0.2 - - - -
999A CYS* 1.3 77.1 - - - +
1001A ALA* 1.4 57.0 + - - +
1003A ARG* 3.4 5.2 + - - +
1004A GLU* 3.0 28.1 + - - +
1007A ILE* 5.4 0.5 - - - +
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Residues in contact with ALA1001 (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 GLN* 3.4 34.1 - - + +
951A ALA 4.0 17.6 - - - +
952A LEU* 3.9 8.0 - - + +
997A PHE 3.3 6.5 + - - +
998A HIS* 5.1 0.2 - - - +
1000A MET* 1.4 76.0 - - - +
1002A GLY* 1.3 64.4 + - - +
1004A GLU* 3.5 18.5 - - - +
1005A GLY 3.9 3.6 + - - -
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Residues in contact with GLY1002 (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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998A HIS* 2.8 25.5 + - - -
999A CYS* 4.0 1.6 - - - -
1001A ALA* 1.3 78.1 - - - +
1003A ARG* 1.4 58.7 + - - +
1005A GLY* 3.8 6.9 + - - -
1006A LEU* 3.9 16.3 + - - +
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Residues in contact with ARG1003 (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 CYS* 3.1 21.6 + - - +
1000A MET* 3.8 4.2 - - - +
1002A GLY* 1.4 70.0 - - - +
1004A GLU* 1.4 57.9 + - - +
1005A GLY 3.1 2.7 - - - -
1006A LEU* 2.9 39.4 + - + +
1007A ILE* 2.9 37.4 + - + +
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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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951A ALA 5.2 1.3 - - - +
952A LEU* 3.7 26.4 - - + -
953A GLU* 3.4 41.3 + - + +
1000A MET 3.0 14.7 + - - +
1001A ALA* 3.5 13.7 - - - +
1002A GLY 3.4 0.2 - - - -
1003A ARG* 1.4 73.7 - - - +
1005A GLY* 1.3 59.2 + - - +
1007A ILE* 3.6 17.6 + - + +
1008A ASP* 3.0 49.0 + - - +
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Residues in contact with GLY1005 (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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1001A ALA 3.9 4.2 + - - -
1002A GLY 3.8 6.3 + - - -
1003A ARG 3.1 1.2 - - - -
1004A GLU* 1.3 78.7 - - - +
1006A LEU* 1.4 61.6 + - - +
1008A ASP* 3.3 12.3 + - - +
1009A THR* 3.0 25.3 + - - -
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Residues in contact with LEU1006 (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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1002A GLY 3.9 17.7 + - - +
1003A ARG* 2.9 23.6 + - + +
1005A GLY* 1.4 69.0 - - - +
1007A ILE* 1.4 63.8 + - + +
1009A THR* 3.3 12.0 + - - +
1010A ALA* 3.2 20.6 + - - +
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Residues in contact with ILE1007 (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 MET 5.4 0.4 - - - +
1003A ARG* 2.9 49.8 + - + +
1004A GLU* 3.7 18.8 - - + +
1005A GLY 3.3 0.2 - - - -
1006A LEU* 1.4 74.0 - - + +
1008A ASP* 1.4 60.3 + - - +
1010A ALA* 3.1 9.8 + - + +
1011A VAL* 2.9 38.0 + - + +
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Residues in contact with ASP1008 (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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1004A GLU* 3.0 35.0 + - - +
1005A GLY* 3.3 12.0 + - - +
1007A ILE* 1.4 81.3 - - - +
1009A THR* 1.4 57.5 + - - +
1011A VAL* 3.0 26.5 - - - +
1012A LYS* 3.4 9.5 - - - +
1202A LEU* 6.0 6.2 - - + +
1203A ASN* 5.2 15.2 + - + +
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Residues in contact with THR1009 (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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1005A GLY 3.0 14.6 + - - -
1006A LEU* 3.5 14.1 - - - +
1007A ILE 3.3 0.4 - - - -
1008A ASP* 1.4 75.8 - - - +
1010A ALA* 1.3 57.1 + - - +
1012A LYS* 3.3 36.5 - - - +
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Residues in contact with ALA1010 (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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1006A LEU 3.2 10.4 + - - +
1007A ILE* 3.1 13.7 + - + +
1009A THR* 1.3 79.1 - - - +
1011A VAL* 1.4 64.5 + - + +
1012A LYS* 3.7 3.3 + - - +
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Residues in contact with VAL1011 (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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1007A ILE* 2.9 26.4 + - + +
1008A ASP* 3.0 15.3 - - - +
1010A ALA* 1.4 80.1 - - + +
1012A LYS* 1.3 56.0 + - - +
1013A THR* 4.2 4.9 - - + +
1203A ASN* 5.9 1.0 + - - -
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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