Contacts of the helix formed by residues 1280 - 1293 (chain D) in PDB entry 7KHC
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 VAL1280 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1261D LEU 5.0 0.7 - - - +
1262D ARG* 3.1 18.2 + - - +
1263D LYS* 4.6 0.2 - - - +
1264D ALA* 4.9 6.1 - - + -
1278D GLU 3.5 2.5 + - - -
1279D GLN* 1.3 72.9 - - - +
1281D GLU* 1.3 70.4 + - + +
1283D SER* 2.9 13.6 + - - +
1284D ARG* 2.9 58.1 + - - +
1302D TYR* 4.3 13.9 - - + -
1304D ARG* 3.4 37.0 - - - +
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Residues in contact with GLU1281 (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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890D THR 4.2 3.2 - - - +
891D ASP* 2.8 30.5 - - + +
892D PHE* 2.2 70.1 + - + -
1258D ARG* 4.4 9.3 + - - -
1262D ARG* 6.2 3.1 - - + -
1279D GLN* 3.0 10.9 - - + -
1280D VAL* 1.3 87.7 - - + +
1282D TYR* 1.3 66.8 + - + +
1284D ARG* 3.7 4.9 + - - +
1285D VAL* 3.0 30.2 + - + +
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Residues in contact with TYR1282 (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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892D PHE* 4.1 23.1 - + - -
1278D GLU* 2.8 32.5 - - + +
1279D GLN* 3.4 14.3 + - - +
1280D VAL 3.5 0.2 - - - -
1281D GLU* 1.3 80.6 - - + +
1283D SER* 1.3 64.1 + - - +
1285D VAL* 3.0 13.6 - - + +
1286D LYS* 2.9 30.2 + - + +
1317D GLU* 3.1 31.1 + - - -
1345D ARG* 3.9 11.6 + - - -
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Residues in contact with SER1283 (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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1264D ALA* 5.4 2.3 - - - +
1266D ILE* 5.5 9.6 - - - -
1278D GLU* 4.7 8.6 - - - +
1279D GLN 3.6 6.2 + - - -
1280D VAL* 2.9 27.2 + - - +
1282D TYR* 1.3 78.1 - - - +
1284D ARG* 1.3 60.6 + - - +
1286D LYS* 3.1 15.6 - - - +
1287D ILE* 2.9 37.0 + - - +
1300D ALA 5.9 0.2 - - - -
1302D TYR* 4.0 22.2 - - - -
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Residues in contact with ARG1284 (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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889D ASP* 4.0 25.0 + - - +
891D ASP* 4.0 20.6 + - - +
1280D VAL* 2.9 34.3 + - - +
1281D GLU* 3.7 5.6 + - - +
1282D TYR 3.2 0.2 - - - -
1283D SER* 1.3 78.9 + - - +
1285D VAL* 1.3 57.6 + - - +
1287D ILE* 3.0 17.1 - - + +
1288D ALA* 2.9 30.8 + - + +
1302D TYR* 3.1 24.2 + - - -
1304D ARG* 3.0 30.9 - - - +
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Residues in contact with VAL1285 (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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891D ASP* 2.9 30.5 - - + +
1281D GLU* 3.0 13.6 + - + +
1282D TYR* 3.0 28.5 - - + +
1284D ARG* 1.3 76.3 - - - +
1286D LYS* 1.3 59.1 + - + +
1288D ALA* 3.2 8.3 + - - +
1289D ASN* 2.9 26.9 + - - +
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Residues in contact with LYS1286 (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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1266D ILE* 5.1 5.6 - - + +
1271D SER* 3.5 36.3 - - - +
1272D SER* 3.7 23.4 + - - +
1282D TYR* 2.9 25.0 + - + +
1283D SER* 3.1 23.1 - - - +
1285D VAL* 1.3 81.1 - - + +
1287D ILE* 1.3 62.1 + - + +
1289D ASN* 3.4 8.5 + - - +
1290D ARG* 2.9 26.5 + - - +
1297D LYS 5.6 3.1 - - - -
1300D ALA* 5.2 13.3 - - - +
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Residues in contact with ILE1287 (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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1283D SER* 2.9 24.0 + - - +
1284D ARG* 3.0 28.3 - - + +
1286D LYS* 1.3 80.4 - - + +
1288D ALA* 1.3 61.0 + - - +
1290D ARG* 3.7 6.6 - - - +
1291D GLU* 2.9 33.1 + - - +
1299D GLY 4.4 2.0 - - - +
1300D ALA* 3.6 37.5 - - + +
1302D TYR* 3.8 27.8 - - + +
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Residues in contact with ALA1288 (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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1284D ARG* 2.9 21.5 + - + +
1285D VAL* 3.2 9.6 + - - +
1287D ILE* 1.3 78.2 - - - +
1289D ASN* 1.3 62.8 + - - +
1291D GLU* 4.0 3.6 - - - +
1292D LEU* 2.9 25.6 + - - +
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Residues in contact with ASN1289 (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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1285D VAL 2.9 13.3 + - - +
1286D LYS* 3.4 12.3 - - - +
1287D ILE 3.2 0.2 - - - -
1288D ALA* 1.3 74.8 - - - +
1290D ARG* 1.3 56.8 + - - +
1292D LEU* 2.8 8.3 + - - +
1293D GLU* 2.6 43.9 + - - +
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Residues in contact with ARG1290 (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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1286D LYS 2.9 19.0 + - - +
1287D ILE* 3.2 5.6 + - - +
1289D ASN* 1.3 73.2 - - - +
1291D GLU* 1.3 53.6 + - - +
1293D GLU* 2.7 27.6 - - - +
1295D ASN 2.6 22.8 - - - +
1296D GLY* 2.9 30.1 - - - +
1297D LYS* 4.8 3.8 - - + +
1299D GLY 3.9 8.5 - - - +
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Residues in contact with GLU1291 (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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1287D ILE 2.9 16.6 + - - +
1288D ALA* 4.1 3.6 - - - +
1290D ARG* 1.3 77.8 - - - +
1292D LEU* 1.3 59.0 + - - +
1293D GLU 3.1 8.5 - - - +
1296D GLY* 5.6 2.2 - - - -
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Residues in contact with LEU1292 (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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1288D ALA 2.9 19.4 + - - +
1289D ASN* 2.8 8.9 + - - +
1291D GLU* 1.3 75.1 - - - +
1293D GLU* 1.3 64.9 + - - +
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Residues in contact with GLU1293 (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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1289D ASN* 2.6 28.4 + - - +
1290D ARG* 2.7 19.4 - - - +
1291D GLU* 3.1 8.1 - - - +
1292D LEU* 1.3 77.6 - - - +
1294D ALA* 1.3 63.5 + - - +
1295D ASN* 4.3 5.4 - - + +
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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