Contacts of the helix formed by residues 1187 - 1200 (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 ASN1187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1100D ARG* 3.5 12.3 - - - +
1101D TYR* 3.7 4.4 + - - -
1186D HIS* 1.3 74.4 - - - +
1188D LEU* 1.3 59.7 + - - +
1189D THR* 3.1 18.5 + - - -
1190D GLU* 3.1 52.0 + - + +
1191D LEU* 2.9 30.5 + - - +
1215D GLY 4.9 2.0 + - - -
1217D ASP* 3.0 33.5 + - + +
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Residues in contact with LEU1188 (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 TYR* 2.7 35.3 + - + +
1131D ILE* 4.1 25.4 - - + -
1164D PHE* 3.8 28.3 - - + -
1165D PRO* 3.9 21.8 - - + -
1169D ALA* 4.5 6.7 - - + -
1186D HIS 3.6 0.4 + - - -
1187D ASN* 1.3 69.4 - - - +
1189D THR* 1.3 66.3 + - - +
1191D LEU* 4.3 4.7 - - + -
1192D ILE* 3.0 39.9 + - + +
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Residues in contact with THR1189 (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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1187D ASN* 3.1 12.6 + - - -
1188D LEU* 1.3 80.0 - - - +
1190D GLU* 1.3 64.5 + - + +
1192D ILE* 4.0 4.1 - - - +
1193D ASN* 3.1 42.4 + - - +
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Residues in contact with GLU1190 (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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1187D ASN* 3.1 32.4 + - + +
1189D THR* 1.3 76.3 - - + +
1191D LEU* 1.3 64.1 + - - +
1193D ASN* 3.4 7.7 + - - +
1194D GLY 3.0 17.3 + - - -
1212D ASP* 3.2 22.3 - - - +
1213D ILE* 3.5 16.8 - - + +
1214D GLU* 3.1 45.5 + - - +
1215D GLY 4.0 10.6 - - - +
1217D ASP* 6.0 0.2 - - - -
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Residues in contact with LEU1191 (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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1165D PRO* 3.9 22.2 - - + +
1168D LEU* 3.7 26.9 - - + -
1169D ALA* 3.4 41.7 - - + +
1186D HIS* 3.7 22.9 - - + -
1187D ASN 2.9 21.4 + - - +
1188D LEU* 3.8 5.2 - - - +
1189D THR 3.3 0.2 - - - -
1190D GLU* 1.3 76.6 - - - +
1192D ILE* 1.3 57.2 + - - +
1194D GLY* 3.0 3.5 + - - -
1195D VAL* 2.9 32.1 + - - +
1213D ILE* 3.9 25.4 - - + -
1348D LEU* 5.3 0.2 - - + -
1352D LEU* 4.6 4.1 - - + +
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Residues in contact with ILE1192 (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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1163D ARG 5.7 1.3 - - - +
1164D PHE* 4.8 6.3 - - + -
1165D PRO* 4.0 23.6 - - + -
1188D LEU* 3.0 41.2 + - + +
1189D THR* 4.1 4.0 - - - +
1191D LEU* 1.3 73.4 - - - +
1193D ASN* 1.3 61.6 + - - +
1195D VAL* 3.1 8.3 + - + +
1196D LEU* 2.8 47.8 + - + +
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Residues in contact with ASN1193 (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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1189D THR* 3.1 34.8 + - - +
1190D GLU* 3.7 6.5 - - - +
1192D ILE* 1.3 77.9 - - - +
1194D GLY* 1.3 57.4 + - - +
1196D LEU* 3.3 18.2 + - - +
1197D SER* 2.8 32.6 + - - -
1212D ASP* 3.8 20.4 + - + +
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Residues in contact with GLY1194 (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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1190D GLU 3.0 12.5 + - - -
1191D LEU 3.0 4.9 + - - -
1193D ASN* 1.3 73.6 - - - +
1195D VAL* 1.3 58.8 + - - +
1197D SER* 3.3 1.0 + - - -
1198D LEU* 2.8 29.5 + - - +
1209D LEU* 3.5 18.1 - - - +
1212D ASP* 3.6 19.4 - - - +
1213D ILE* 4.4 7.2 - - - -
1352D LEU* 4.8 3.4 - - - -
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Residues in contact with VAL1195 (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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1165D PRO* 4.8 4.9 - - + -
1191D LEU 2.9 20.5 + - - +
1192D ILE* 3.1 11.0 + - + +
1194D GLY* 1.3 74.4 - - - +
1196D LEU* 1.3 61.0 + - + +
1198D LEU* 3.3 7.6 + - - +
1199D SER* 2.8 28.5 + - - -
1352D LEU* 3.8 26.5 - - + +
1355D TYR* 4.2 27.4 - - + -
1356D LEU* 4.2 32.5 - - + +
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Residues in contact with LEU1196 (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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1192D ILE* 2.8 34.5 + - + +
1193D ASN* 3.6 22.0 - - - +
1195D VAL* 1.3 79.6 - - + +
1197D SER* 1.3 59.7 + - - +
1199D SER* 2.6 27.3 + - - +
1200D LYS* 3.3 31.6 + - - +
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Residues in contact with SER1197 (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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1193D ASN 2.8 12.0 + - - -
1194D GLY 3.3 4.0 + - - -
1196D LEU* 1.3 74.8 - - - +
1198D LEU* 1.3 62.6 + - - +
1200D LYS* 3.3 11.3 + - - +
1201D ASN* 3.2 22.2 + - - +
1204D ILE* 3.9 20.1 - - - +
1209D LEU* 4.8 0.2 - - - -
1212D ASP* 2.7 32.3 + - - -
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Residues in contact with LEU1198 (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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1194D GLY 2.8 16.7 + - - +
1195D VAL* 3.3 6.0 + - - +
1197D SER* 1.3 77.7 - - - +
1199D SER* 1.3 62.6 + - - +
1201D ASN 3.0 26.6 + - - +
1202D PRO* 3.6 10.3 - - + +
1204D ILE* 3.8 25.7 - - + +
1209D LEU* 4.5 5.4 - - + -
1349D LYS* 4.2 11.7 - - + +
1352D LEU* 3.7 35.9 - - + +
1353D VAL* 3.8 30.5 - - + -
1356D LEU* 4.0 17.1 - - + +
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Residues in contact with SER1199 (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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1195D VAL* 2.8 17.8 + - - -
1196D LEU* 2.6 29.8 + - - +
1198D LEU* 1.3 74.6 - - - +
1200D LYS* 1.3 65.1 + - - +
1202D PRO* 5.0 4.7 - - - +
1356D LEU* 3.8 26.5 - - - -
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Residues in contact with LYS1200 (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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1196D LEU* 3.4 34.5 - - - +
1197D SER* 3.3 9.9 + - - +
1198D LEU 3.1 0.6 - - - -
1199D SER* 1.3 82.0 - - - +
1201D ASN* 1.3 61.4 + - + +
1202D PRO* 4.1 4.1 - - - +
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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