Contacts of the helix formed by residues 1113 - 1125 (chain D) in PDB entry 2CKJ
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 SER1113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1112D GLY* 1.4 74.6 - - - +
1114D TRP* 1.3 60.0 + - - +
1115D GLU* 3.2 19.4 - - - +
1116D ASP* 2.9 45.0 + - - +
1117D TRP* 3.0 10.3 + - - -
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Residues in contact with TRP1114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024D VAL* 3.9 30.3 - - + -
1028D GLY* 2.9 26.0 + - - -
1030D VAL* 4.2 4.0 - - + -
1055D LEU* 4.3 23.3 - - + -
1057D ILE* 3.6 48.1 - - + +
1061D LYS* 4.2 12.9 - - + +
1098D ILE* 5.0 4.5 - - + -
1099D LEU* 5.8 5.2 - - + -
1102D LEU* 3.8 30.3 - - + -
1112D GLY 3.8 1.2 + - - -
1113D SER* 1.3 67.9 - - - +
1115D GLU* 1.4 85.1 + - - +
1116D ASP 3.0 1.6 - - - -
1117D TRP* 3.4 29.3 + + + +
1118D VAL* 3.1 28.0 + - + +
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Residues in contact with GLU1115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026D THR 5.4 1.0 - - - +
1027D ASP 4.1 20.6 - - - +
1028D GLY* 4.5 6.7 - - - +
1061D LYS* 2.5 40.2 + - - -
1113D SER* 3.5 18.9 - - - +
1114D TRP* 1.4 77.3 + - - +
1116D ASP* 1.3 58.2 + - - +
1118D VAL* 3.1 6.0 + - - +
1119D THR* 2.8 40.6 + - - +
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Residues in contact with ASP1116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D ASN* 3.9 18.6 + - - +
1112D GLY* 4.1 4.0 - - - -
1113D SER* 2.9 42.6 + - - +
1115D GLU* 1.3 85.7 - - - +
1117D TRP* 1.3 59.7 + - + +
1119D THR* 3.6 7.1 + - - -
1120D ALA* 3.4 20.6 + - - +
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Residues in contact with TRP1117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102D LEU* 3.8 20.8 - - + +
1105D TYR* 3.5 28.8 - - + +
1106D LYS* 3.2 50.7 - - + +
1109D ASN* 3.5 26.3 + - + +
1110D PRO 4.4 10.1 - - - -
1112D GLY 3.3 21.9 + - - -
1113D SER 3.0 11.4 + - - -
1114D TRP* 3.4 37.4 + + + +
1115D GLU 3.3 0.2 - - - -
1116D ASP* 1.3 77.2 - - + +
1118D VAL* 1.4 60.5 + - - +
1120D ALA* 3.7 6.5 - - + +
1121D ALA* 3.1 28.2 + - - +
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Residues in contact with VAL1118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024D VAL* 4.2 9.6 - - + -
1025D TYR 4.2 17.9 - - - +
1026D THR* 4.9 7.4 - - - +
1028D GLY* 5.1 5.6 - - - +
1102D LEU* 4.7 11.4 - - + -
1114D TRP* 3.1 47.8 - - + +
1115D GLU* 3.1 7.9 + - - +
1117D TRP* 1.4 72.3 - - - +
1119D THR* 1.4 57.2 + - - +
1120D ALA 2.6 16.2 + - - -
1121D ALA* 3.0 10.9 + - - +
1122D TYR* 3.1 13.0 + - + +
1128D LEU* 3.5 30.1 - - + -
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Residues in contact with THR1119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026D THR* 3.9 27.4 + - + +
1115D GLU* 2.8 29.0 + - - +
1116D ASP* 3.6 7.4 + - - -
1118D VAL* 1.4 72.0 - - - +
1120D ALA* 1.3 58.4 + - - +
1122D TYR* 4.1 7.2 - - + +
1123D MET* 2.9 39.7 + - + +
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Residues in contact with ALA1120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105D TYR* 4.2 17.3 - - + -
1116D ASP 3.4 17.2 + - - +
1117D TRP* 3.7 8.3 - - - +
1118D VAL 2.6 6.3 + - - -
1119D THR* 1.3 79.8 - - - +
1121D ALA* 1.4 56.2 - - - +
1123D MET* 3.3 4.7 + - - +
1124D ASP* 3.2 26.7 + - - +
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Residues in contact with ALA1121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101D ARG 5.5 0.7 - - - +
1102D LEU* 3.8 20.9 - - + -
1105D TYR* 4.0 17.8 - - + -
1117D TRP 3.1 14.9 + - - +
1118D VAL 3.0 3.0 + - - +
1120D ALA* 1.4 75.5 - - - +
1122D TYR* 1.4 53.8 + - - +
1124D ASP 3.4 0.3 + - - -
1125D THR 2.6 30.8 + - - -
1126D VAL* 2.8 34.8 + - + +
1128D LEU* 4.7 8.1 - - + -
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Residues in contact with TYR1122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771C MET* 4.1 19.5 - - + +
1014C PHE* 4.6 23.3 - + - +
1015C LEU* 3.9 19.9 - - - +
1017C GLN* 3.4 35.8 + - - +
1074C ASN* 4.1 27.3 + - + -
1076C SER* 4.4 6.9 + - - -
1026D THR* 3.9 29.4 - - + -
1118D VAL* 3.1 14.2 + - + +
1119D THR* 4.1 9.2 - - + +
1121D ALA* 1.4 74.3 - - - +
1123D MET* 1.3 71.5 + - + +
1125D THR* 2.9 20.8 + - - -
1126D VAL 4.8 4.3 - - - +
1128D LEU* 4.4 14.4 - - + +
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Residues in contact with MET1123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014C PHE* 3.4 57.0 - - + +
1119D THR* 2.9 27.3 + - + +
1120D ALA* 3.3 4.7 + - - +
1121D ALA 3.3 0.6 - - - -
1122D TYR* 1.3 87.5 - - + +
1124D ASP* 1.3 60.4 + - - +
1125D THR* 4.8 0.3 + - - -
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Residues in contact with ASP1124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135C ARG* 4.4 16.8 + - - -
1105D TYR* 2.7 36.9 + - + +
1108D LYS* 5.5 4.8 + - - -
1120D ALA 3.2 15.3 + - - +
1121D ALA 3.4 1.8 - - - +
1122D TYR 3.1 0.4 - - - -
1123D MET* 1.3 78.6 - - - +
1125D THR* 1.3 71.7 + - - +
1126D VAL* 5.0 0.2 - - - +
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Residues in contact with THR1125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014C PHE* 4.4 12.8 + - - +
1016C ASN 5.0 1.9 + - - -
1017C GLN* 3.9 24.8 + - + +
1133C PHE* 4.3 14.9 - - + -
1135C ARG* 3.0 53.5 + - + +
1121D ALA 2.6 12.7 + - - -
1122D TYR 2.9 10.1 + - - -
1124D ASP* 1.3 83.6 - - - +
1126D VAL* 1.3 59.1 + - - +
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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