Contacts of the helix formed by residues 1073 - 1086 (chain D) in PDB entry 1KF9
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 LEU1073 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071D SER* 3.0 7.6 + - - +
1072D ASN* 1.3 77.6 - - - +
1074D GLU* 1.3 63.9 + - + +
1075D LEU 3.0 4.3 - - - -
1076D LEU* 3.1 13.8 + - - +
1077D ARG* 3.2 37.3 + - - +
1125D MET* 3.9 16.4 - - + +
1128D LEU* 3.4 47.3 - - + -
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Residues in contact with GLU1074 (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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1069D GLN 4.2 2.3 - - - +
1070D LYS* 3.3 33.6 + - + +
1071D SER* 2.9 42.9 + - - +
1073D LEU* 1.3 73.4 - - + +
1075D LEU* 1.3 58.5 + - - +
1077D ARG* 4.0 14.2 - - - +
1078D ILE* 2.8 33.9 + - - +
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Residues in contact with LEU1075 (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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1061D PRO* 4.8 2.0 - - + -
1067D THR* 3.8 25.6 - - + +
1070D LYS* 3.7 20.9 - - + -
1071D SER 3.1 11.3 + - - +
1072D ASN 4.4 0.2 - - - +
1073D LEU 3.0 0.6 - - - -
1074D GLU* 1.3 79.8 - - - +
1076D LEU* 1.3 58.6 + - - +
1077D ARG 3.2 0.4 - - - -
1078D ILE* 3.6 11.7 + - + +
1079D SER* 3.1 30.3 + - - -
1176D TYR* 4.2 24.2 - - + +
1177D LEU* 5.6 0.7 - - - -
1179D THR* 3.9 15.5 - - + -
1180D VAL* 3.5 27.6 - - + -
1183D ARG* 3.3 29.2 - - - +
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Residues in contact with LEU1076 (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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1072D ASN 2.8 25.1 - - - +
1073D LEU* 3.1 8.7 + - - +
1075D LEU* 1.3 77.2 - - - +
1077D ARG* 1.3 58.7 + - - +
1079D SER* 3.7 4.0 - - - -
1080D LEU* 2.9 21.7 + - - +
1121D ILE* 3.1 25.3 - - + +
1124D LEU* 3.9 32.8 - - + -
1125D MET* 4.1 19.2 - - + +
1128D LEU* 3.4 24.5 - - + -
1177D LEU* 3.4 28.5 - - + -
1180D VAL* 4.5 11.2 - - + -
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Residues in contact with ARG1077 (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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1073D LEU* 3.2 47.0 + - - +
1074D GLU* 4.0 11.4 - - - +
1076D LEU* 1.3 75.1 - - - +
1078D ILE* 1.3 58.3 + - + +
1079D SER 3.1 0.7 - - - -
1080D LEU* 3.8 2.9 - - + +
1081D LEU* 2.7 61.0 + - + +
1125D MET* 3.7 31.4 - - + +
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Residues in contact with ILE1078 (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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1058D ILE* 4.3 3.4 - - + -
1059D PRO* 3.4 31.9 - - + +
1060D THR* 3.5 18.2 - - + -
1061D PRO* 4.0 25.1 - - + -
1070D LYS* 4.5 13.9 - - - -
1074D GLU* 2.8 24.2 + - + +
1075D LEU* 3.8 13.9 - - + +
1076D LEU 3.5 0.2 - - - -
1077D ARG* 1.3 76.5 - - + +
1079D SER* 1.3 53.6 + - - +
1081D LEU* 3.5 8.8 - - + +
1082D LEU* 2.8 43.0 + - + +
1176D TYR* 3.6 17.0 - - + -
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Residues in contact with SER1079 (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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1075D LEU 3.1 17.6 + - - -
1076D LEU 3.7 5.2 - - - -
1078D ILE* 1.3 80.0 - - - +
1080D LEU* 1.3 56.9 + - - +
1082D LEU* 3.6 3.0 + - - +
1083D ILE* 2.9 35.6 + - - +
1121D ILE* 4.5 4.0 - - - -
1173D VAL* 3.7 20.9 - - - +
1176D TYR* 3.4 24.9 - - - +
1177D LEU* 3.9 21.9 - - - +
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Residues in contact with LEU1080 (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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1076D LEU 2.9 21.7 + - - +
1077D ARG* 3.0 5.4 + - + +
1079D SER* 1.3 72.8 - - - +
1081D LEU* 1.3 61.1 + - + +
1083D ILE* 3.5 3.3 + - + -
1084D GLN* 2.8 52.8 + - - +
1118D GLU* 3.2 38.4 - - + +
1121D ILE* 3.4 14.3 - - + +
1122D GLN* 3.6 26.0 - - + -
1125D MET* 4.1 21.5 - - + -
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Residues in contact with LEU1081 (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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1058D ILE* 3.7 28.7 - - + +
1059D PRO* 5.3 8.5 - - + -
1077D ARG* 2.7 49.1 + - + +
1078D ILE* 3.5 8.5 - - + +
1080D LEU* 1.3 71.6 - - + +
1082D LEU* 1.3 65.8 + - - +
1084D GLN* 3.4 17.6 + - - +
1085D SER* 3.0 23.0 + - - -
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Residues in contact with LEU1082 (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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1055D SER* 3.6 30.3 - - - +
1058D ILE* 4.0 12.3 - - + -
1060D THR* 4.3 9.0 - - + -
1078D ILE* 2.8 29.5 + - + +
1079D SER 3.6 4.3 - - - +
1081D LEU* 1.3 77.0 - - - +
1083D ILE* 1.3 63.1 + - - +
1085D SER* 2.5 25.3 + - - -
1086D TRP* 3.3 8.8 - - - -
1169D ASP* 4.2 17.3 - - + +
1170D MET* 5.9 0.7 - - + -
1172D LYS* 3.9 17.7 - - + +
1173D VAL* 4.1 13.7 - - + -
1176D TYR* 3.9 27.6 - - + -
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Residues in contact with ILE1083 (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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1079D SER 2.9 27.2 + - - +
1080D LEU* 3.6 7.4 - - + +
1082D LEU* 1.3 75.1 - - - +
1084D GLN* 1.3 59.9 + - - +
1086D TRP* 3.0 26.6 + - - +
1087D LEU* 3.6 7.8 + - + +
1114D LEU* 3.6 46.2 - - + +
1117D LEU* 3.4 25.8 - - + -
1118D GLU* 4.1 16.2 - - + -
1121D ILE* 4.0 15.3 - - + -
1170D MET* 4.3 9.2 - - + -
1173D VAL* 3.8 17.5 - - + -
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Residues in contact with GLN1084 (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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1080D LEU* 2.8 47.9 + - + +
1081D LEU* 3.8 21.6 - - - +
1082D LEU 3.4 0.2 - - - -
1083D ILE* 1.3 73.0 - - - +
1085D SER* 1.3 62.4 + - - +
1086D TRP 2.9 6.8 + - - -
1087D LEU* 3.2 29.3 + - + +
1088D GLU 4.7 0.9 + - - -
1118D GLU* 3.1 27.2 - - + +
1122D GLN* 4.3 4.0 - - - +
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Residues in contact with SER1085 (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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1054D PRO* 3.9 24.3 + - - +
1055D SER* 3.6 18.7 - - - -
1058D ILE* 4.2 5.2 - - - -
1081D LEU 3.0 14.4 + - - -
1082D LEU 2.5 20.6 + - - -
1084D GLN* 1.3 75.3 - - - +
1086D TRP* 1.3 68.5 + - - +
1089D PRO* 3.3 20.3 - - - +
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Residues in contact with TRP1086 (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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1054D PRO* 3.7 15.5 - - + +
1055D SER* 4.1 0.2 + - - -
1082D LEU 3.3 9.0 - - - -
1083D ILE 3.0 9.8 + - - +
1084D GLN 2.9 1.0 - - - -
1085D SER* 1.3 99.3 + - - +
1087D LEU* 1.3 63.2 + - - +
1088D GLU 3.3 3.1 - - - -
1089D PRO* 3.6 8.1 - - + -
1090D VAL* 3.0 45.8 + - + +
1093D LEU* 4.5 7.9 - - + -
1114D LEU* 4.5 14.1 - - + -
1162D LEU* 3.4 35.0 - - + -
1165D CYS* 3.3 13.7 - - + -
1166D PHE* 3.1 61.2 - + + -
1169D ASP* 2.6 36.1 + - + +
1170D MET* 4.3 7.2 - - + -
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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