Contacts of the helix formed by residues 1082 - 1094 (chain D) in PDB entry 5NPK
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 GLY1082 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122B ARG* 4.3 17.9 - - - -
1081D HIS* 1.3 78.4 - - - +
1083D ASP* 1.3 64.6 + - - -
1084D SER* 3.2 6.1 - - - -
1085D SER* 3.2 21.8 + - - -
1086D ILE* 3.6 6.6 + - - +
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Residues in contact with ASP1083 (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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1122B ARG* 3.7 24.5 + - - +
1071D VAL* 3.8 21.3 - - + +
1075D MET* 3.8 21.7 - - + +
1081D HIS 3.4 1.8 + - - -
1082D GLY* 1.3 70.1 - - - -
1084D SER* 1.3 71.6 + - - +
1086D ILE* 3.1 4.3 + - - +
1087D TYR* 2.8 32.2 + - - +
1121D MET* 3.8 23.0 - - + +
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Residues in contact with SER1084 (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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1082D GLY* 3.2 3.5 - - - -
1083D ASP* 1.3 86.7 + - - +
1085D SER* 1.3 62.4 + - - +
1087D TYR* 4.5 5.8 - - - +
1088D GLU* 2.9 51.6 + - - +
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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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1045D VAL* 4.3 4.8 - - - +
1079D HIS* 5.3 5.8 - - - -
1081D HIS* 5.2 7.1 - - - +
1082D GLY* 3.2 16.9 + - - -
1084D SER* 1.3 84.0 + - - +
1086D ILE* 1.3 62.6 + - - +
1088D GLU* 4.4 2.9 - - - +
1089D ALA* 3.3 24.1 + - - +
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Residues in contact with ILE1086 (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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1045D VAL* 4.0 7.6 - - + -
1049D ILE* 3.4 19.9 - - + +
1071D VAL* 3.8 24.0 - - + +
1074D VAL* 4.0 19.5 - - + -
1075D MET* 3.5 39.0 - - + +
1079D HIS* 3.5 41.7 - - + +
1081D HIS 4.1 0.4 - - - +
1082D GLY 3.6 11.4 + - - +
1083D ASP* 3.1 5.7 + - - +
1085D SER* 1.3 77.2 - - - +
1087D TYR* 1.3 64.2 + - - +
1089D ALA 3.3 1.7 + - - -
1090D MET* 3.0 18.2 + - - +
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Residues in contact with TYR1087 (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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1067D SER* 3.6 15.5 - - - -
1071D VAL* 4.0 16.2 - - + -
1083D ASP 2.8 21.0 + - - +
1084D SER* 4.2 4.5 - - - +
1086D ILE* 1.3 75.0 - - - +
1088D GLU* 1.3 64.4 + - + +
1090D MET* 3.0 19.9 + - + +
1091D VAL* 2.8 51.4 + - + +
1110D PHE* 4.8 1.9 - + - -
1118D ALA* 3.9 9.8 - - + +
1119D ALA 2.7 29.7 + - - -
1120D ALA* 4.3 1.6 - - - -
1121D MET* 3.4 39.2 - - + -
1124D THR* 2.7 22.6 + - - +
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Residues in contact with GLU1088 (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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1084D SER* 2.9 35.2 + - - +
1085D SER* 4.4 3.2 - - - +
1087D TYR* 1.3 83.9 - - + +
1089D ALA* 1.3 61.5 + - - +
1091D VAL* 3.4 10.1 + - + +
1092D ARG* 3.1 26.6 + - - +
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Residues in contact with ALA1089 (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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1045D VAL* 4.1 12.1 - - + -
1046D HIS* 3.8 23.8 - - + +
1049D ILE* 4.0 11.0 - - + -
1085D SER 3.3 18.3 + - - +
1086D ILE 3.6 4.0 - - - +
1087D TYR 3.2 0.4 - - - -
1088D GLU* 1.3 76.7 - - - +
1090D MET* 1.3 64.0 + - - +
1092D ARG* 3.3 9.3 + - - +
1093D MET* 3.3 27.7 + - - +
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Residues in contact with MET1090 (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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1049D ILE* 3.8 24.5 - - + +
1053D LEU* 5.4 2.2 - - - -
1067D SER* 3.6 32.5 - - - +
1070D ILE* 4.1 27.1 - - - -
1071D VAL* 4.8 5.8 - - + -
1086D ILE 3.0 12.2 + - - +
1087D TYR* 3.0 23.8 + - + +
1089D ALA* 1.3 75.7 - - - +
1091D VAL* 1.3 64.6 + - - +
1093D MET* 3.2 20.3 + - - +
1094D ALA* 3.3 10.0 + - - +
1104D VAL* 3.9 18.2 - - + +
1110D PHE* 4.3 11.2 - - + -
1126D ALA* 3.9 21.8 - - + -
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Residues in contact with VAL1091 (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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1087D TYR* 2.8 43.8 + - + +
1088D GLU* 3.6 11.4 - - + +
1090D MET* 1.3 77.0 - - - +
1092D ARG* 1.3 63.6 + - + +
1094D ALA* 3.0 14.4 + - - +
1095D GLN* 3.4 34.3 + - - +
1110D PHE* 3.6 25.3 - - + +
1118D ALA* 3.7 29.4 - - + +
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Residues in contact with ARG1092 (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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1046D HIS* 5.4 5.8 + - - +
1088D GLU 3.1 14.3 + - - +
1089D ALA* 3.7 11.7 - - - +
1090D MET 3.3 0.2 - - - -
1091D VAL* 1.3 75.8 - - + +
1093D MET* 1.3 61.8 + - - +
1094D ALA 3.1 1.3 + - - -
1095D GLN* 3.2 27.9 + - - +
1098D SER* 3.7 29.9 + - - +
1099D TYR* 3.1 44.8 + - + +
1172D ALA* 6.3 0.8 - - - +
1173D SER* 5.8 7.5 + - - +
1266D PHE* 6.0 3.4 - - - -
1267D GLN* 5.2 12.4 - - - +
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Residues in contact with MET1093 (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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1046D HIS* 3.9 24.7 - - + -
1049D ILE* 3.7 44.6 - - + -
1050D LEU* 4.0 19.7 - - - -
1089D ALA 3.3 17.2 + - - +
1090D MET* 3.2 6.9 + - - +
1092D ARG* 1.3 75.7 - - - +
1094D ALA* 1.3 56.2 + - - +
1095D GLN 3.5 0.4 - - - -
1099D TYR* 3.5 33.4 - - + +
1102D PRO* 3.5 7.4 - - - +
1103D LEU* 2.9 43.8 + - + -
1104D VAL* 3.1 18.2 + - + -
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Residues in contact with ALA1094 (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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1090D MET 3.3 3.2 + - - +
1091D VAL 3.0 11.0 + - - +
1093D MET* 1.3 78.4 - - - +
1095D GLN* 1.3 60.0 + - - +
1096D ASP* 3.7 2.4 + - - +
1102D PRO* 4.7 5.5 - - - +
1104D VAL* 3.2 35.3 - - + +
1106D GLY* 4.2 8.4 + - - +
1110D PHE* 3.7 26.8 - - + +
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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