Contacts of the helix formed by residues 1212 - 1220 (chain B) in PDB entry 2RFI
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 GLY1212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170B HIS* 4.4 0.6 - - - -
1210B ASP* 3.0 22.0 + - - -
1211B TYR* 1.3 79.2 - - - +
1213B GLU* 1.3 68.0 + - - -
1214B ARG 3.4 3.4 - - - -
1215B PHE* 3.3 9.5 + - - +
1216B TRP* 3.4 20.4 - - - -
1234B HIS* 5.5 0.9 - - - -
8Q SER* 4.2 9.9 - - - -
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Residues in contact with GLU1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212B GLY* 1.3 67.9 - - - -
1214B ARG* 1.3 58.3 + - + +
1215B PHE 3.1 5.2 - - - -
1216B TRP* 4.6 2.9 - - - +
1217B ASP* 3.1 53.2 + - - +
1233B ARG* 4.2 17.7 + - - -
1234B HIS* 4.3 15.0 + - - -
8Q SER* 4.8 1.6 + - - -
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Residues in contact with ARG1214 (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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1145B ASP* 2.8 46.0 + - - +
1146B LEU 5.3 3.6 + - - -
1153B VAL* 6.2 1.2 - - - +
1212B GLY 3.4 1.2 - - - -
1213B GLU* 1.3 77.7 - - + +
1215B PHE* 1.3 56.4 + - - +
1217B ASP* 4.7 4.5 - - - -
1218B ILE* 4.1 8.8 - - - +
4Q THR 4.4 1.6 - - - +
5Q ALA* 3.7 5.5 - - - -
6Q ARG* 3.1 35.0 + - + +
8Q SER* 3.4 31.7 + - - -
9Q THR* 4.5 9.9 + - - +
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Residues in contact with PHE1215 (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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102A SAH 4.0 8.3 - - - -
1140B ASP 5.3 0.7 - - - -
1141B SER* 4.2 22.2 - - - -
1211B TYR* 3.4 48.9 - + + +
1212B GLY 3.3 9.5 + - - +
1213B GLU 3.1 0.6 - - - -
1214B ARG* 1.3 78.7 - - - +
1216B TRP* 1.3 83.4 + + - +
1217B ASP 3.3 0.2 - - - -
1218B ILE* 3.1 8.7 + - - +
1219B LYS* 2.9 56.3 + - + +
1223B PHE* 4.0 17.0 - + - -
5Q ALA* 4.0 14.8 - - + +
6Q ARG 3.2 13.9 + - - +
7Q MLY 4.1 13.0 - - + -
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Residues in contact with TRP1216 (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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102A SAH 4.4 6.1 - + - -
1170B HIS* 3.1 54.4 + + + -
1211B TYR* 4.4 0.4 - - + -
1212B GLY 3.4 24.8 + - - +
1213B GLU* 4.6 2.5 - - - +
1215B PHE* 1.3 92.3 - + - +
1217B ASP* 1.3 63.1 + - - +
1218B ILE 3.0 2.0 - - - -
1219B LYS 4.4 0.9 - - - -
1220B GLY* 2.8 43.7 + - - +
1221B LYS* 5.7 0.2 - - - +
1223B PHE* 3.6 44.9 - + - -
1224B SER* 4.3 0.7 - - - -
1225B CYS* 3.7 31.4 - - + -
1234B HIS* 3.5 46.9 - + + +
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Residues in contact with ASP1217 (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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1213B GLU* 3.1 38.7 + - - +
1214B ARG* 5.1 3.2 - - - -
1216B TRP* 1.3 76.5 - - - +
1218B ILE* 1.3 67.5 + - + +
1221B LYS* 3.5 28.9 + - - +
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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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1140B ASP* 4.0 9.0 - - - +
1214B ARG 4.1 8.5 - - - +
1215B PHE 3.1 5.1 + - - +
1216B TRP 3.0 0.2 - - - -
1217B ASP* 1.3 89.9 - - + +
1219B LYS* 1.3 66.1 + - + +
1220B GLY 3.4 1.2 + - - -
1221B LYS* 3.6 24.9 + - - +
1222B LEU* 4.6 6.7 + - + +
4Q THR* 4.0 15.7 - - - +
5Q ALA* 4.0 33.2 - - + +
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Residues in contact with LYS1219 (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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1139B GLU* 4.3 2.6 + - - -
1140B ASP* 2.7 38.2 + - - -
1141B SER* 3.5 23.9 + - - +
1215B PHE* 2.9 50.5 + - + +
1216B TRP* 4.4 2.2 - - + -
1218B ILE* 1.3 77.0 - - + +
1220B GLY* 1.3 65.1 + - - +
1221B LYS 3.1 2.0 - - - -
1222B LEU* 3.1 33.7 + - + +
1223B PHE* 3.1 40.5 + - + +
5Q ALA* 3.8 7.9 - - + -
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Residues in contact with GLY1220 (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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1216B TRP* 2.8 31.5 + - - -
1219B LYS* 1.3 77.8 - - - +
1221B LYS* 1.3 57.2 + - - +
1222B LEU 3.1 3.1 + - - -
1223B PHE 3.1 21.2 + - - +
1224B SER* 5.1 1.8 - - - -
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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