Contacts of the helix formed by residues 1213 - 1221 (chain B) in PDB entry 4E70
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 ASN1213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1112B PRO 5.8 0.8 + - - -
1180B ALA* 2.9 37.6 + - - +
1183B SER* 3.8 17.7 - - - -
1184B TRP* 4.0 24.8 - - - +
1187B SER* 3.9 2.8 + - - -
1188B ARG* 5.4 0.5 + - - -
1209B GLY 4.4 1.8 + - - -
1211B THR* 3.6 7.9 + - - +
1212B GLY* 1.3 76.8 - - - +
1214B THR* 1.3 63.6 + - - +
1216B LYS* 3.9 2.2 - - - +
1217B VAL* 3.5 25.1 + - - +
1241B GLN* 2.6 37.0 + - - +
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Residues in contact with THR1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183B SER* 3.4 23.8 + - - -
1186B PHE* 6.0 1.0 - - + -
1187B SER* 3.9 18.8 - - - -
1190B LEU* 4.8 8.5 - - + -
1206B ASP* 3.6 12.3 - - - +
1209B GLY* 5.3 2.7 + - - -
1212B GLY 3.3 0.4 - - - -
1213B ASN* 1.3 78.0 - - - +
1215B SER* 1.3 63.8 + - - +
1217B VAL* 3.3 5.9 + - - +
1218B ILE* 3.1 39.0 + - + +
1265B LEU* 3.9 17.0 - - + -
1267B LYS* 4.1 17.6 - - + +
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Residues in contact with SER1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B LEU* 4.4 2.3 - - - +
1206B ASP* 2.7 36.4 + - - +
1212B GLY 3.4 2.7 + - - -
1214B THR* 1.3 76.0 - - - +
1216B LYS* 1.3 59.7 + - - +
1218B ILE* 3.7 8.8 - - - +
1219B ALA* 2.8 32.7 + - - +
1227B CYS* 3.9 16.2 - - - +
1229B VAL* 3.6 7.9 - - - +
1246B LEU* 3.6 27.1 - - - -
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Residues in contact with LYS1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212B GLY 2.9 19.5 + - - +
1213B ASN 3.9 5.8 - - - +
1215B SER* 1.3 77.1 - - - +
1217B VAL* 1.3 61.0 + - + +
1219B ALA* 3.8 3.1 - - - +
1220B GLU* 3.0 63.2 + - + +
1241B GLN* 3.9 33.2 - - + +
1242B THR 2.6 30.7 + - - +
1243B HIS* 3.8 21.3 - - + +
1246B LEU* 4.2 6.0 - - + +
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Residues in contact with VAL1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187B SER* 3.3 50.7 - - - +
1188B ARG* 3.3 38.6 - - + +
1191B VAL* 4.0 14.6 - - + -
1213B ASN 3.5 8.4 + - - +
1214B THR 3.3 1.7 + - - +
1215B SER 3.2 0.4 - - - -
1216B LYS* 1.3 77.1 - - + +
1218B ILE* 1.3 64.7 + - - +
1220B GLU* 3.8 11.5 - - - +
1221B THR* 2.8 34.1 + - - +
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Residues in contact with ILE1218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187B SER* 5.7 0.9 - - - -
1190B LEU* 4.9 2.5 - - + -
1191B VAL* 4.1 17.7 - - + -
1198B PHE* 3.9 39.9 - - + -
1204B LEU* 4.1 13.0 - - + -
1214B THR* 3.1 35.6 + - + +
1215B SER* 3.7 7.4 - - - +
1217B VAL* 1.3 75.1 - - - +
1219B ALA* 1.3 59.0 + - - +
1221B THR 3.2 0.7 + - - -
1222B PHE* 2.8 32.4 + - + +
1225B ILE* 4.2 13.5 - - + -
1227B CYS* 3.8 16.4 - - - -
1265B LEU* 3.9 17.9 - - + -
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Residues in contact with ALA1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B SER 2.8 20.8 + - - +
1216B LYS 3.8 3.1 - - - +
1218B ILE* 1.3 74.3 - - - +
1220B GLU* 1.3 62.9 + - - +
1222B PHE 3.4 20.9 - - - +
1223B PRO* 3.7 8.1 - - - +
1225B ILE 4.4 7.4 - - - +
1227B CYS* 4.3 13.9 - - + -
1243B HIS* 3.6 36.2 + - + +
1245B ASN* 4.5 8.4 + - + +
1246B LEU* 5.0 1.3 - - + -
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Residues in contact with GLU1220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188B ARG* 4.8 6.6 + - - -
1216B LYS* 3.0 49.7 + - - +
1217B VAL* 3.8 17.1 - - - +
1218B ILE 3.3 0.2 - - - -
1219B ALA* 1.3 77.3 - - - +
1221B THR* 1.3 62.4 + - - +
1223B PRO* 4.8 5.9 - - - +
1243B HIS* 3.9 21.5 - - + +
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Residues in contact with THR1221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191B VAL* 3.5 26.0 - - + +
1195B ARG* 4.0 21.7 + - - +
1217B VAL* 2.8 24.6 + - - +
1220B GLU* 1.3 80.8 - - - +
1222B PHE* 1.3 90.1 + - + +
1223B PRO* 3.5 7.8 - - - +
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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