Contacts of the helix formed by residues 1210 - 1218 (chain B) in PDB entry 5YWB
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 GLY1210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778B TRP* 3.6 37.4 - - - -
1206B GLU 3.0 11.9 + - - -
1207B THR 3.9 4.3 - - - -
1209B GLU* 1.3 75.1 - - - +
1211B LEU* 1.3 62.8 + - - +
1212B THR* 3.5 3.5 + - - -
1213B THR 3.6 4.1 + - - -
1214B ILE* 3.5 23.9 + - - +
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Residues in contact with LEU1211 (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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399B ILE* 4.0 31.9 - - + +
400B MET* 4.6 17.5 - - + -
402B LEU* 4.4 14.4 - - + -
404B THR* 5.3 1.8 - - - +
407B LEU* 4.8 13.0 - - + -
1207B THR* 3.7 15.2 + - + +
1208B VAL* 3.3 24.0 - - + +
1209B GLU 2.9 7.7 + - - +
1210B GLY* 1.3 76.0 - - - +
1212B THR* 1.3 67.8 + - + +
1214B ILE* 3.1 5.1 + - + -
1215B ARG* 3.0 57.0 + - - +
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Residues in contact with THR1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B THR* 4.2 25.4 - - + +
724B LEU* 4.3 26.5 - - + -
727B LEU* 4.5 3.8 - - - +
729B GLU* 4.6 16.8 - - + +
772B TYR* 4.1 20.4 - - - -
774B SER* 4.2 11.8 + - - +
1209B GLU 4.9 0.9 + - - -
1210B GLY* 4.9 1.7 - - - -
1211B LEU* 1.3 79.5 + - + +
1213B THR* 1.3 57.0 + - - +
1215B ARG* 3.4 2.0 + - - +
1216B ALA* 2.9 31.7 + - - +
1480B GLU* 5.9 0.2 - - - +
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Residues in contact with THR1213 (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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772B TYR* 3.9 23.4 + - - +
773B ALA* 5.3 0.2 - - - -
774B SER* 4.6 8.3 + - - -
778B TRP* 3.6 33.3 + - + +
790B PHE* 4.7 10.5 - - + -
842B ARG* 5.0 8.3 - - - +
1210B GLY 3.6 2.5 + - - -
1211B LEU 3.2 0.6 - - - -
1212B THR* 1.3 81.0 + - - +
1214B ILE* 1.3 64.6 + - - +
1216B ALA* 3.1 5.7 + - - +
1217B PHE* 3.0 56.8 + - + -
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Residues in contact with ILE1214 (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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400B MET* 4.1 22.0 - - + -
778B TRP* 3.7 24.5 - - + -
790B PHE* 4.7 4.0 - - + -
1207B THR* 4.2 24.5 - - + +
1210B GLY 3.5 12.1 + - - +
1211B LEU* 3.1 8.3 + - + +
1213B THR* 1.3 75.4 - - - +
1215B ARG* 1.3 61.1 + - - +
1217B PHE* 3.8 3.4 + - - +
1218B ARG* 3.4 16.3 + - - -
1219B TYR* 3.5 9.3 + - + -
1220B GLU* 4.4 7.2 - - - +
1223B PHE* 3.5 58.8 - - + -
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Residues in contact with ARG1215 (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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400B MET* 2.8 33.5 + - + -
401B HIS* 4.0 5.2 + - - +
402B LEU* 2.4 32.8 + - - +
403B SER* 4.2 1.8 - - - +
404B THR* 3.8 14.6 + - - +
619B ILE* 4.4 10.9 - - - +
727B LEU 5.3 2.6 - - - +
729B GLU* 2.9 45.5 + - - +
1211B LEU* 3.0 43.6 + - - +
1212B THR 3.7 0.9 - - - +
1214B ILE* 1.3 76.0 - - - +
1216B ALA* 1.3 62.7 + - - +
1218B ARG* 3.9 17.2 + - - +
1220B GLU* 3.4 28.2 - - - +
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Residues in contact with ALA1216 (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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727B LEU* 3.6 36.3 - - + -
770B VAL* 3.4 32.7 + - - +
772B TYR* 4.2 11.4 - - + -
1212B THR 2.9 17.6 + - - +
1213B THR* 3.1 5.1 + - - +
1215B ARG* 1.3 76.0 - - - +
1217B PHE* 1.3 67.4 + - + +
1218B ARG* 3.0 12.3 + - - +
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Residues in contact with PHE1217 (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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769B PRO* 3.3 23.1 - - + +
770B VAL 3.8 9.4 - - - +
771B ALA* 3.8 22.9 - - + -
772B TYR* 4.0 17.7 - - - -
790B PHE* 4.5 14.6 - + + -
842B ARG* 4.8 13.5 - - - -
843B ALA* 4.8 6.1 - - - -
846B GLN* 3.6 35.0 - - + -
1213B THR* 3.0 49.2 + - + +
1214B ILE 4.3 1.6 - - - +
1216B ALA* 1.3 78.0 - - + +
1218B ARG* 1.3 67.3 + - - +
1219B TYR* 3.6 39.0 - + + +
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Residues in contact with ARG1218 (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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622B GLU* 4.7 6.1 + - - -
727B LEU 4.1 12.4 + - - -
728B GLY* 5.2 1.8 - - - -
739B TRP* 3.6 27.7 - - - +
768B GLY* 2.4 47.7 + - - +
769B PRO* 4.8 3.3 - - + +
770B VAL* 3.8 7.5 - - - +
1214B ILE 3.4 8.0 + - - -
1215B ARG 3.9 13.6 + - - +
1216B ALA 3.0 17.7 + - - +
1217B PHE* 1.3 80.7 - - - +
1219B TYR* 1.3 58.8 + - - +
1220B GLU* 3.3 21.1 + - - +
1221B ALA* 5.1 0.9 + - - +
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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