Contacts of the helix formed by residues 1207 - 1219 (chain B) in PDB entry 5XA0
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 ASN1207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1203B ARG* 2.5 35.0 + - + +
1206B ARG* 1.3 75.3 - - - +
1208B MET* 1.3 57.2 + - - +
1211B HIS* 2.5 40.8 - - - +
1250B GLN* 6.2 2.5 - - + -
1254B LEU* 4.3 16.9 - - + +
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Residues in contact with MET1208 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1203B ARG 4.5 0.4 + - - -
1207B ASN* 1.3 77.6 - - - +
1209B GLY* 1.3 58.2 + - - +
1211B HIS* 4.6 0.9 - - - -
1212B ALA* 2.9 34.8 + - - +
1254B LEU* 5.0 9.8 - - - +
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Residues in contact with GLY1209 (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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1123B ARG* 6.0 0.7 - - - -
1206B ARG* 4.0 10.8 - - - +
1207B ASN 4.1 2.2 - - - +
1208B MET* 1.3 79.0 - - - +
1210B ALA* 1.3 50.3 + - - +
1212B ALA* 4.9 1.6 - - - -
1213B VAL* 2.3 41.1 + - - +
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Residues in contact with ALA1210 (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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1123B ARG* 4.7 10.5 - - + -
1206B ARG* 2.9 44.0 - - + +
1207B ASN* 4.2 0.2 - - - -
1208B MET 3.2 0.4 - - - -
1209B GLY* 1.3 77.7 - - - +
1211B HIS* 1.3 56.8 + - - +
1213B VAL* 4.2 1.3 - - - -
1214B VAL* 2.4 43.5 + - + +
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Residues in contact with HIS1211 (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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1207B ASN* 2.5 26.3 + - - +
1208B MET 4.1 1.1 - - - +
1210B ALA* 1.3 77.2 - - - +
1212B ALA* 1.3 57.6 + - - +
1214B VAL* 4.7 0.9 - - - -
1215B LEU* 2.8 34.0 + - - +
1254B LEU* 4.5 19.1 - - + +
1255B LEU* 4.7 14.6 - - + -
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Residues in contact with ALA1212 (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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1208B MET 2.9 18.0 + - - +
1209B GLY* 4.8 1.6 - - - +
1211B HIS* 1.3 76.1 - - - +
1213B VAL* 1.3 65.4 + - - +
1215B LEU* 3.8 3.9 - - - +
1216B GLU* 3.0 23.0 + - - +
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Residues in contact with VAL1213 (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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1123B ARG 5.4 2.9 - - - +
1126B VAL 5.0 1.6 - - - -
1127B GLU* 4.3 23.9 - - + +
1130B GLU* 3.6 13.2 - - - +
1209B GLY* 2.3 33.2 + - - +
1210B ALA* 4.2 1.3 - - - -
1212B ALA* 1.3 77.9 - - - +
1214B VAL* 1.3 64.0 + - - +
1216B GLU* 3.0 21.0 + - - +
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Residues in contact with VAL1214 (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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1126B VAL* 4.9 13.9 - - + -
1130B GLU* 4.4 7.1 - - - +
1210B ALA* 2.4 37.1 + - + +
1211B HIS* 4.3 0.7 - - - +
1213B VAL* 1.3 74.2 - - - +
1215B LEU* 1.3 56.8 + - - +
1216B GLU 3.2 0.3 + - - -
1217B LEU 3.7 0.7 + - - -
1218B LEU* 2.8 28.3 + - - +
1233B ILE* 3.5 22.8 - - - +
1234B MET 3.7 9.9 - - - +
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Residues in contact with LEU1215 (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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1211B HIS 2.8 22.9 + - - +
1212B ALA* 3.8 4.9 - - - +
1214B VAL* 1.3 79.3 - - - +
1216B GLU* 1.4 58.5 + - - +
1218B LEU* 2.8 29.3 + - + +
1219B GLN* 3.3 7.4 + - - +
1220B ILE 4.6 0.5 + - - -
1234B MET* 4.6 3.1 + - + +
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Residues in contact with GLU1216 (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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1130B GLU* 5.1 2.0 - - + -
1131B LEU* 5.8 2.5 - - - +
1212B ALA 3.0 13.3 + - - +
1213B VAL* 3.0 17.4 + - - +
1215B LEU* 1.4 76.2 - - - +
1217B LEU* 1.3 58.4 + - - +
1220B ILE* 3.0 23.6 + - - +
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Residues in contact with LEU1217 (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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1130B GLU* 2.4 53.7 - - - +
1131B LEU* 4.6 0.2 - - - -
1133B VAL 3.1 7.1 - - - +
1134B TYR* 3.6 17.3 - - - +
1214B VAL 3.7 2.4 + - - -
1216B GLU* 1.3 76.3 - - - +
1218B LEU* 1.3 66.0 + - - +
1219B GLN 3.0 2.6 + - - +
1220B ILE* 4.0 9.6 + - + +
1221B PRO* 4.6 6.9 - - + +
1230B MET* 3.7 5.2 - - - +
1233B ILE* 4.6 0.2 - - - -
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Residues in contact with LEU1218 (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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1214B VAL 2.8 15.3 + - - +
1215B LEU* 2.8 19.0 + - + +
1217B LEU* 1.3 78.3 - - - +
1219B GLN* 1.3 59.8 + - + +
1230B MET* 2.3 39.9 - - - +
1231B GLN* 3.0 4.7 + - - -
1233B ILE* 4.2 0.6 - - - +
1234B MET* 2.8 41.3 - - + +
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Residues in contact with GLN1219 (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 LEU 3.3 5.2 + - - +
1218B LEU* 1.3 86.8 - - + +
1220B ILE* 1.3 64.7 + - - +
1221B PRO 3.2 7.6 - - - +
1222B TYR* 4.7 1.2 + - - -
1230B MET* 3.4 8.1 - - + -
1234B MET* 5.8 0.4 - - + -
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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