Contacts of the helix formed by residues 990 - 1004 (chain A) in PDB entry 3NC0
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 GLN 990 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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988A HIS 3.8 1.2 + - - -
989A LEU* 1.3 74.3 - - - +
991A ASP* 1.3 58.1 + - - +
992A ALA* 4.0 18.1 - - - +
993A GLN* 2.7 65.6 + - + +
994A VAL* 3.4 4.1 + - - +
1026A ALA* 4.6 3.1 - - - -
1027A GLY 2.8 30.0 - - - +
1028A GLU* 3.5 39.8 - - + +
1030A THR 3.9 6.3 + - - +
1031A SER* 4.2 18.2 + - - +
1033A LEU* 5.6 8.1 - - - +
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Residues in contact with ASP 991 (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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983A LYS* 3.1 40.1 + - - +
989A LEU 3.9 1.1 + - - +
990A GLN* 1.3 72.5 - - - +
992A ALA* 1.3 56.5 + - - +
994A VAL* 3.3 8.1 + - - +
995A LYS* 2.8 33.8 + - + +
1028A GLU* 4.1 12.7 + - - +
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Residues in contact with ALA 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 GLN* 2.8 23.6 + - + +
991A ASP* 1.3 74.1 - - - +
993A GLN* 1.3 65.7 + - - +
995A LYS* 4.0 5.6 - - - +
996A LEU* 3.0 27.3 + - - +
1033A LEU* 5.6 1.3 - - + -
1035A LEU* 4.7 25.5 - - + +
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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
----------------------------------------------------------
988A HIS 4.5 0.2 - - - +
989A LEU* 3.3 24.2 - - + +
990A GLN* 2.7 52.6 + - + +
992A ALA* 1.3 76.0 - - - +
994A VAL* 1.3 62.0 + - - +
996A LEU* 3.5 5.2 + - - +
997A PHE* 3.2 19.4 + - - +
1018A PHE* 5.1 3.0 - - + -
1021A GLN* 3.2 49.7 + - - +
1026A ALA* 3.4 31.5 - - - +
1027A GLY 5.0 0.2 + - - -
1033A LEU* 4.5 15.9 - - + +
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Residues in contact with VAL 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A ALA* 4.0 27.1 - - + +
982A LEU* 4.5 9.9 - - + -
983A LYS* 4.3 24.5 - - + +
989A LEU* 4.0 34.8 - - + -
990A GLN 3.4 4.0 + - - +
991A ASP* 3.3 7.7 + - - +
992A ALA 3.3 0.2 - - - -
993A GLN* 1.3 73.0 - - - +
995A LYS* 1.3 68.2 + - - +
997A PHE* 2.8 17.5 + - - +
998A VAL* 2.9 28.9 + - + +
1018A PHE* 4.8 4.5 - - + -
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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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979A ALA* 5.9 1.6 - - - -
991A ASP* 2.8 23.2 + - + +
992A ALA* 4.0 5.4 - - - +
994A VAL* 1.3 73.8 - - - +
996A LEU* 1.3 59.2 - - - +
998A VAL* 3.5 6.9 + - - +
999A THR* 2.8 41.9 + - - +
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Residues in contact with LEU 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 ALA 3.0 17.7 + - - +
993A GLN 3.5 5.4 - - - +
995A LYS* 1.3 76.9 - - - +
997A PHE* 1.3 63.0 + - - +
999A THR* 3.2 7.4 + - - -
1000A GLY* 3.1 17.8 + - - -
1014A HIS* 4.2 5.3 - - + -
1033A LEU* 4.1 26.9 - - + -
1034A PHE 5.2 0.7 - - - +
1035A LEU* 4.1 22.7 - - + -
1038A ARG* 4.3 25.1 - - + +
1039A GLU* 5.0 8.7 - - + -
1042A LEU* 3.7 23.8 - - + -
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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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927A PHE* 3.8 15.9 - + - -
930A VAL* 6.1 0.4 - - + -
982A LEU* 3.5 32.5 - - + -
993A GLN 3.2 9.7 + - - +
994A VAL 2.8 9.4 + - - +
996A LEU* 1.3 79.3 - - - +
998A VAL* 1.3 63.1 + - - +
1000A GLY 3.0 6.2 + - - -
1001A LEU* 3.3 19.0 + - + +
1014A HIS* 2.8 66.7 + + - -
1015A LEU* 3.9 22.2 - - + -
1018A PHE* 3.3 52.3 - + + -
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Residues in contact with VAL 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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975A GLN* 3.3 45.5 - - + +
978A VAL* 4.1 16.2 - - + -
979A ALA* 3.9 31.0 - - + +
982A LEU* 4.3 5.6 - - + -
994A VAL* 2.9 28.4 + - + +
995A LYS* 4.0 5.8 - - - +
997A PHE* 1.3 71.3 - - - +
999A THR* 1.3 61.2 + - - +
1001A LEU* 3.2 24.9 + - + +
1002A PHE* 3.4 12.0 - - + -
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Residues in contact with THR 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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975A GLN* 4.1 13.8 + - - +
995A LYS* 2.8 35.4 + - - +
996A LEU* 3.5 7.7 - - - -
998A VAL* 1.3 77.1 - - - +
1000A GLY* 1.3 59.9 + - - +
1001A LEU 3.1 1.5 + - - -
1002A PHE* 3.3 11.5 + - - +
1003A SER* 3.0 15.2 + - - +
1042A LEU* 4.9 8.7 - - + -
1043A ARG* 3.3 30.5 + - - +
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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 LEU 3.1 6.7 + - - -
997A PHE 3.0 10.6 + - - -
999A THR* 1.3 76.6 - - - +
1001A LEU* 1.3 56.8 + - - +
1002A PHE 3.2 0.2 - - - -
1003A SER* 3.1 11.4 - - - -
1004A LEU* 3.0 39.2 + - - +
1011A PHE* 4.6 0.3 - - - -
1014A HIS* 3.9 14.8 - - - -
1042A LEU* 3.8 15.2 - - - +
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Residues in contact with LEU1001 (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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927A PHE* 3.8 18.4 - - + -
950A PHE* 3.4 50.0 - - + +
978A VAL* 4.4 8.1 - - + -
997A PHE* 3.4 27.1 - - + +
998A VAL* 3.3 23.6 - - + +
999A THR 3.1 1.0 - - - -
1000A GLY* 1.3 78.8 - - - +
1002A PHE* 1.3 64.0 + - + +
1004A LEU 4.6 0.7 - - - -
1005A ASN* 3.7 9.0 - - - +
1011A PHE* 3.7 31.9 - - + -
1014A HIS* 3.8 19.3 - - + -
1015A LEU* 5.0 3.1 - - + -
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Residues in contact with PHE1002 (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 PHE* 3.7 30.7 - + + -
953A VAL* 3.9 15.7 - - + -
954A GLU* 3.2 24.4 - - + +
971A GLN* 3.7 34.8 - - + +
974A ILE* 3.3 30.1 - - + -
975A GLN* 3.2 31.0 - - + +
978A VAL* 6.1 0.4 - - + -
998A VAL* 3.4 20.6 - - + -
999A THR 3.3 6.4 + - - +
1000A GLY 3.2 0.2 - - - -
1001A LEU* 1.3 79.5 - - + +
1003A SER* 1.3 60.1 + - - +
1004A LEU 3.7 0.2 - - - -
1005A ASN* 3.0 20.6 - - - +
1043A ARG* 5.7 3.4 - - - +
1046A GLN* 3.0 10.4 + - - -
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Residues in contact with SER1003 (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 THR 3.0 16.8 + - - -
1000A GLY* 3.1 14.6 + - - -
1002A PHE* 1.3 78.3 - - - +
1004A LEU* 1.3 59.4 + - - +
1005A ASN* 3.1 9.4 + - - +
1006A GLN* 4.6 0.7 + - - +
1042A LEU* 3.7 33.0 - - - +
1043A ARG* 4.4 8.7 - - - -
1045A ALA* 4.1 5.2 - - - +
1046A GLN* 3.0 40.0 + - - +
1049A LYS* 4.2 3.3 - - - +
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Residues in contact with LEU1004 (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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1000A GLY 3.0 20.7 + - - +
1003A SER* 1.3 75.0 - - - +
1005A ASN* 1.3 55.9 + - - +
1006A GLN 2.9 12.0 + - - -
1007A ASP* 3.2 19.3 + - + +
1010A ALA* 4.0 24.0 - - + +
1011A PHE* 3.6 25.9 - - + +
1014A HIS* 3.5 36.8 - - + -
1038A ARG* 3.8 16.2 - - - +
1041A ALA 5.8 0.4 - - - +
1042A LEU* 3.9 22.9 - - + +
1045A ALA* 4.2 20.6 - - + -
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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