Contacts of the helix formed by residues 1249 - 1261 (chain D) in PDB entry 7KHE
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 ASN1249 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494D ALA 3.5 22.5 + - - +
495D ASN* 5.0 6.3 - - + +
837D ASP 5.7 3.0 + - - -
838D ARG 5.5 2.6 - - - +
840D LEU 5.0 9.5 + - - -
842D ARG* 4.9 4.9 + - - +
902D ASP* 3.2 26.0 + - - +
1248D ILE* 1.3 81.7 - - - +
1250D ASP* 1.3 83.6 + - - +
1251D LYS* 3.0 24.6 + - - +
1252D HIS* 3.4 21.3 + - + +
1253D ILE* 4.4 1.6 + - - +
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Residues in contact with ASP1250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822D MET* 4.4 9.5 - - + +
838D ARG* 3.9 33.8 + - - +
842D ARG* 4.8 5.7 + - - +
1234D VAL* 4.1 21.4 - - + +
1238D GLN* 3.1 31.8 + - - +
1248D ILE 4.0 1.7 - - - +
1249D ASN* 1.3 82.0 + - - +
1251D LYS* 1.3 61.9 + - - +
1252D HIS 3.0 0.9 + - - -
1253D ILE* 3.1 8.6 + - - +
1254D GLU* 2.9 32.8 + - - +
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Residues in contact with LYS1251 (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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840D LEU 5.8 1.1 - - - -
841D GLY 4.1 5.6 + - - -
842D ARG* 3.7 35.2 - - - +
885D VAL* 4.5 1.7 - - + +
899D TYR* 3.1 59.6 + - + +
901D ARG 3.8 6.5 - - - +
902D ASP* 3.1 45.5 - - - +
1249D ASN* 3.0 18.6 + - + +
1250D ASP* 1.3 77.7 - - - +
1252D HIS* 1.3 59.7 + - + +
1254D GLU* 3.2 10.3 + - - +
1255D VAL* 2.9 34.8 + - + +
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Residues in contact with HIS1252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D PRO 3.5 23.4 + - - -
494D ALA 3.6 9.6 + - - -
899D TYR* 3.9 21.6 + - - -
902D ASP* 4.7 3.8 + - - -
915D ILE* 5.0 1.0 - - - +
918D ILE* 4.2 12.8 - - + +
919D ALA* 3.2 37.3 + - + +
922D SER* 3.7 19.7 + - - -
923D ILE* 3.6 19.1 - - + -
1248D ILE* 3.9 7.2 - - + -
1249D ASN* 3.4 25.0 - - + +
1250D ASP 3.0 1.0 + - - -
1251D LYS* 1.3 76.2 - - + +
1253D ILE* 1.3 67.3 + - - +
1255D VAL* 3.0 22.3 - - - +
1256D ILE* 3.1 8.1 + - - +
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Residues in contact with ILE1253 (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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923D ILE* 3.7 19.0 - - + +
1145D PHE* 4.2 17.5 - - + -
1233D ILE* 4.8 0.7 - - + -
1234D VAL* 4.1 21.1 - - + +
1237D VAL* 3.6 40.2 - - + -
1238D GLN* 3.2 31.6 - - - +
1241D TYR* 4.7 9.0 - - + -
1248D ILE* 4.9 4.9 - - + -
1249D ASN 4.6 4.7 - - - +
1250D ASP* 3.1 8.5 + - - +
1252D HIS* 1.3 75.7 - - - +
1254D GLU* 1.3 56.8 + - - +
1256D ILE* 3.3 5.0 + - - +
1257D VAL* 2.9 38.3 + - + +
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Residues in contact with GLU1254 (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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820D ILE* 3.7 16.1 - - - +
822D MET* 4.9 2.1 - - - +
842D ARG* 3.2 35.2 + - - -
884D SER* 3.4 19.1 - - - -
885D VAL* 3.8 17.4 + - + +
886D VAL* 4.6 6.8 + - + +
1230D THR* 4.4 9.6 - - - +
1234D VAL* 4.0 19.0 - - + +
1250D ASP* 2.9 21.0 + - - +
1251D LYS* 3.4 11.0 - - - +
1252D HIS 3.0 0.2 - - - -
1253D ILE* 1.3 74.1 - - - +
1255D VAL* 1.3 66.1 + - - +
1257D VAL* 3.2 8.6 + - - +
1258D ARG* 2.9 22.5 + - - +
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Residues in contact with VAL1255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804D ALA* 5.3 1.3 - - + -
807D LEU* 3.9 23.2 - - + +
885D VAL* 3.8 26.7 - - + -
899D TYR* 4.7 4.9 - - + -
915D ILE* 4.4 19.7 - - + +
916D GLY* 4.9 3.4 - - - +
919D ALA* 3.2 24.7 - - + -
1251D LYS 2.9 16.7 + - - +
1252D HIS* 3.0 18.4 + - - +
1254D GLU* 1.3 74.8 - - - +
1256D ILE* 1.3 69.6 + - + +
1258D ARG* 3.1 7.4 + - - +
1259D GLN* 2.9 25.0 + - - +
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Residues in contact with ILE1256 (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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800D LEU* 3.9 35.4 - - + +
803D VAL* 4.4 5.2 - - + -
804D ALA* 4.0 26.5 - - + -
920D ALA* 4.8 6.7 - - - -
923D ILE* 3.6 21.5 - - + -
1145D PHE* 4.9 15.3 - - + -
1252D HIS 3.1 13.3 + - - +
1253D ILE* 3.4 7.9 - - - +
1255D VAL* 1.3 81.3 - - + +
1257D VAL* 1.3 58.9 + - + +
1259D GLN* 2.7 24.3 + - + +
1260D MET* 3.0 15.9 + - + +
1309D ILE* 4.2 17.7 - - + -
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Residues in contact with VAL1257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886D VAL* 5.0 2.0 - - + -
1145D PHE* 5.9 0.9 - - + -
1229D VAL* 5.3 2.7 - - + -
1230D THR* 3.8 36.6 - - - +
1233D ILE* 3.9 31.4 - - + -
1234D VAL* 4.6 3.1 - - + -
1253D ILE* 2.9 31.4 + - + +
1254D GLU* 3.2 6.9 + - - +
1256D ILE* 1.3 72.9 - - + +
1258D ARG* 1.3 62.7 + - - +
1260D MET* 3.0 29.5 + - + +
1261D LEU* 3.2 26.9 + - + +
1306D LEU* 5.7 0.2 - - + -
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Residues in contact with ARG1258 (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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807D LEU* 3.9 14.5 - - - +
885D VAL* 4.1 16.2 + - + +
886D VAL* 4.0 35.9 + - + +
888D CYS* 4.7 10.6 + - - +
890D THR 3.6 17.8 + - - -
891D ASP* 4.9 4.9 - - - +
892D PHE 5.0 3.0 - - - +
893D GLY 3.0 24.0 + - - +
894D VAL* 3.2 21.6 - - - +
1254D GLU 2.9 12.4 + - - +
1255D VAL* 3.1 11.6 + - - +
1257D VAL* 1.3 76.6 - - - +
1259D GLN* 1.3 71.7 + - - +
1261D LEU* 3.2 14.5 + - + +
1262D ARG* 3.6 9.2 + - - +
1280D VAL* 6.2 2.4 - - - +
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Residues in contact with GLN1259 (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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803D VAL* 3.5 32.6 + - + +
804D ALA* 4.1 17.9 - - + -
806D ASP* 6.1 3.6 - - - +
807D LEU* 3.2 32.8 - - + +
1255D VAL 2.9 12.9 + - - +
1256D ILE* 2.7 18.8 + - - +
1258D ARG* 1.3 79.6 + - - +
1260D MET* 1.3 59.0 + - - -
1261D LEU 3.5 0.3 + - - -
1262D ARG* 3.0 61.9 + - - +
1312D ALA* 4.1 10.9 - - - +
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Residues in contact with MET1260 (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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803D VAL* 5.7 0.2 - - + -
1144D LEU 5.5 2.7 - - - +
1145D PHE* 3.6 29.8 - - + +
1147D ALA* 5.2 4.7 - - + -
1233D ILE* 4.8 15.5 - - + -
1256D ILE* 3.0 19.1 + - + +
1257D VAL* 3.0 28.4 + - + +
1259D GLN* 1.3 80.3 - - + +
1261D LEU* 1.3 60.4 + - + +
1262D ARG* 3.2 3.6 + - - +
1263D LYS* 6.0 0.2 - - - +
1305D ASP 3.9 0.9 - - - +
1306D LEU* 3.9 24.4 - - + -
1307D LEU* 3.2 52.0 + - - +
1308D GLY* 4.7 0.7 - - - -
1309D ILE* 3.8 21.5 - - + -
1312D ALA* 4.7 4.4 - - - +
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Residues in contact with LEU1261 (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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886D VAL* 4.5 9.6 - - + -
1221D LEU* 3.5 32.1 - - + -
1226D VAL* 3.7 30.1 - - + -
1229D VAL* 4.4 8.1 - - + -
1230D THR* 5.8 0.2 - - - -
1257D VAL* 3.4 21.3 - - + +
1258D ARG* 3.2 9.4 + - + +
1260D MET* 1.3 76.0 - - + +
1262D ARG* 1.3 59.3 + - - +
1263D LYS 2.8 17.3 + - - +
1280D VAL* 4.7 1.0 - - - +
1304D ARG* 3.6 31.0 + - - +
1305D ASP 3.7 6.1 - - - +
1306D LEU* 3.8 27.8 - - + -
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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