Contacts of the helix formed by residues 1071 - 1080 (chain A) in PDB entry 4KSC
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 GLY1071 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048A VAL* 4.7 4.2 - - - +
1049A LEU* 4.3 17.3 - - - +
1064A LEU* 4.5 5.4 - - - +
1070A CYS* 1.3 75.6 - - - +
1072A LYS* 1.3 64.2 + - - +
1073A SER 4.1 0.2 - - - +
1074A THR* 3.0 21.5 + - - +
1075A VAL* 3.3 21.8 - - - +
1242A ILE* 4.9 13.8 - - - +
1244A ASN* 6.6 0.2 - - - -
1245A GLY 6.0 0.9 - - - -
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Residues in contact with LYS1072 (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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1064A LEU* 4.1 14.7 - - + +
1065A VAL* 4.9 3.3 - - - +
1066A GLY* 3.0 49.3 + - - +
1067A SER 3.9 10.0 + - - -
1068A SER* 4.3 8.7 - - - +
1069A GLY 4.0 16.6 - - - +
1070A CYS 2.9 6.5 + - - +
1071A GLY* 1.3 81.0 - - - +
1073A SER* 1.3 63.3 + - - +
1074A THR 3.6 0.2 + - - -
1075A VAL* 3.7 11.1 + - - +
1076A VAL 4.1 1.7 + - - -
1197A GLU* 5.0 13.2 + - - +
1226A ILE* 3.6 47.0 + - + +
1228A HIS* 3.3 33.3 + - - +
1242A ILE* 5.4 0.6 - - + +
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Residues in contact with SER1073 (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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1069A GLY 3.8 15.0 + - - -
1070A CYS* 5.1 6.5 - - - -
1071A GLY 4.1 0.6 - - - +
1072A LYS* 1.3 76.0 - - - +
1074A THR* 1.3 66.3 + - - +
1076A VAL* 3.2 7.4 + - - +
1077A GLN* 3.1 34.8 + - - +
1196A ASP* 3.7 23.3 + - - +
1197A GLU* 4.3 6.9 + - - -
1226A ILE* 3.8 10.3 - - - +
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Residues in contact with THR1074 (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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1038A PHE* 3.8 24.9 - - + -
1040A TYR* 6.2 1.1 - - + -
1048A VAL* 4.2 6.3 - - + -
1049A LEU* 3.1 18.7 - - - +
1070A CYS* 3.8 31.4 - - + -
1071A GLY* 3.0 21.1 + - - +
1073A SER* 1.3 74.3 - - - +
1075A VAL* 1.3 58.7 + - - +
1077A GLN* 2.9 18.4 + - - +
1078A LEU* 2.7 40.4 + - - +
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Residues in contact with VAL1075 (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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1033A PHE* 4.1 28.1 - - + -
1049A LEU* 5.0 2.2 - - + -
1052A LEU* 4.1 25.8 - - + -
1054A LEU* 5.3 5.6 - - + -
1064A LEU* 5.6 11.2 - - + -
1071A GLY 3.3 17.9 - - - +
1072A LYS 3.7 8.7 + - - +
1073A SER 3.3 0.4 - - - -
1074A THR* 1.3 83.9 + - - +
1076A VAL* 1.3 67.7 + - + +
1078A LEU* 3.3 11.7 + - + +
1079A LEU* 3.2 22.0 + - + +
1224A ILE* 5.1 17.9 - - + -
1226A ILE* 6.0 0.7 - - + -
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Residues in contact with VAL1076 (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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1072A LYS 4.2 10.3 - - - +
1073A SER* 3.2 10.4 + - - +
1075A VAL* 1.3 79.8 - - + +
1077A GLN* 1.3 64.4 + - + +
1079A LEU* 3.3 14.4 + - - +
1080A GLU* 3.3 16.4 + - + +
1111A ILE* 3.6 30.3 - - + -
1194A LEU* 3.7 32.1 - - + -
1195A LEU 5.1 3.4 - - - +
1196A ASP* 4.9 10.1 - - + +
1224A ILE* 5.1 5.6 - - + +
1226A ILE* 4.2 23.6 - - + -
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Residues in contact with GLN1077 (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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258A ARG* 3.6 26.0 + - - +
1038A PHE* 5.5 5.0 - - + -
1073A SER* 3.1 23.6 + - - +
1074A THR* 2.9 22.4 + - - +
1076A VAL* 1.3 79.9 - - + +
1078A LEU* 1.3 65.0 + - + +
1080A GLU* 3.1 15.5 + - - +
1082A PHE* 3.2 46.5 + - + +
1196A ASP* 5.8 1.4 + - - +
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Residues in contact with LEU1078 (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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1033A PHE* 5.4 11.4 - - + -
1036A VAL* 4.6 16.2 - - + -
1038A PHE* 3.5 56.8 - - + -
1049A LEU* 4.7 8.5 - - + -
1052A LEU* 6.5 0.4 - - + -
1074A THR 2.7 27.1 + - - +
1075A VAL* 3.7 9.6 - - + +
1077A GLN* 1.3 74.8 - - + +
1079A LEU* 1.3 57.6 + - - +
1081A ARG* 2.8 22.5 + - - +
1082A PHE* 4.6 0.9 - - + +
1083A TYR* 3.5 22.4 - - + +
1085A PRO* 5.3 6.7 - - + -
1090A VAL* 5.4 5.4 - - - +
1097A ILE* 5.2 5.4 - - - +
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Residues in contact with LEU1079 (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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1031A VAL* 4.6 25.4 - - + -
1033A PHE* 5.2 7.1 - - + -
1075A VAL* 3.2 12.2 + - + +
1076A VAL* 3.5 11.9 - - - +
1077A GLN 3.2 0.2 - - - -
1078A LEU* 1.3 72.6 - - - +
1080A GLU* 1.3 61.7 + - - +
1081A ARG 3.0 5.5 + - - -
1090A VAL* 5.1 12.6 - - + -
1091A PHE 6.6 0.2 - - - -
1092A LEU* 5.9 2.5 - - + -
1097A ILE* 5.2 7.6 - - + -
1105A LEU* 3.8 30.0 - - + +
1109A LEU* 4.6 8.1 - - + +
1192A ILE* 4.0 22.9 - - + -
1194A LEU* 3.7 36.1 - - + -
1224A ILE* 4.8 9.4 - - + -
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Residues in contact with GLU1080 (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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262A ALA* 3.6 21.8 - - - +
1076A VAL* 3.3 15.9 - - + +
1077A GLN* 3.1 8.0 + - - +
1079A LEU* 1.3 76.0 - - - +
1081A ARG* 1.3 65.8 + - - +
1082A PHE* 3.4 33.2 + - + -
1105A LEU* 4.7 1.9 - - - +
1106A ARG* 3.1 28.4 + - + +
1109A LEU* 3.1 40.1 - - + +
1111A ILE* 4.2 16.3 - - + +
1194A LEU* 3.2 26.3 - - - +
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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