Contacts of the helix formed by residues 1246 - 1255 (chain D) in PDB entry 6CSU
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 ARG1246 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1243B GLU* 3.6 28.7 + - - +
1246B ARG* 4.5 20.6 - - - +
498C ALA* 6.0 3.3 - - - +
500C LEU* 3.7 24.7 - - + +
1242D ALA 3.5 13.5 - - - +
1243D GLU* 2.8 39.1 + - - +
1245D LEU* 1.3 75.5 - - - +
1247D GLU* 1.3 62.6 + - - +
1248D ARG 3.2 0.2 - - - -
1249D GLN* 3.4 43.3 + - - +
1250D GLU* 3.8 3.1 + - - +
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Residues in contact with GLU1247 (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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498A ALA* 4.7 8.9 - - - +
1243D GLU* 3.2 9.1 + - + +
1244D VAL* 3.2 42.2 + - - +
1246D ARG* 1.3 72.0 - - - +
1248D ARG* 1.3 55.7 + - - +
1249D GLN 3.1 1.8 - - - -
1250D GLU* 2.8 13.0 + - + +
1251D THR* 2.6 47.4 + - + +
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Residues in contact with ARG1248 (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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1244D VAL 3.8 2.8 + - - +
1245D LEU* 3.2 48.3 + - - +
1246D ARG 3.2 0.4 - - - -
1247D GLU* 1.3 76.4 - - - +
1249D GLN* 1.3 53.6 + - + +
1251D THR* 3.0 9.9 + - - +
1252D ALA* 2.7 37.2 + - - +
1255D MET* 5.3 0.2 - - - +
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Residues in contact with GLN1249 (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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1245D LEU 5.3 1.5 + - - +
1246D ARG* 3.4 38.8 + - - +
1247D GLU 3.1 0.6 - - - -
1248D ARG* 1.3 81.1 - - + +
1250D GLU* 1.3 56.7 + - - +
1252D ALA* 3.7 5.9 - - - +
1253D ARG* 3.1 25.8 + - - +
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Residues in contact with GLU1250 (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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1246B ARG* 5.4 1.9 + - - +
1249B GLN* 5.2 5.6 + - - -
1250B GLU* 2.8 30.0 - - - +
1253B ARG* 5.9 0.6 - - - -
1246D ARG 3.8 2.1 + - - +
1247D GLU* 2.8 19.8 + - + +
1249D GLN* 1.3 77.2 - - - +
1251D THR* 1.3 63.5 + - + +
1253D ARG* 3.0 11.1 + - - +
1254D LYS* 2.9 28.3 + - + +
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Residues in contact with THR1251 (chain D).
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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1247D GLU* 2.6 30.1 + - + +
1248D ARG* 3.0 20.4 + - - +
1250D GLU* 1.3 75.9 - - + +
1252D ALA* 1.3 55.4 + - - +
1254D LYS* 3.2 9.3 + - - +
1255D MET* 3.0 41.9 + - - +
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Residues in contact with ALA1252 (chain D).
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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1248D ARG 2.7 23.2 + - - +
1249D GLN* 3.7 7.0 - - - +
1251D THR* 1.3 71.5 + - - +
1253D ARG* 1.3 64.8 + - - +
1255D MET* 3.1 34.7 + - + +
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Residues in contact with ARG1253 (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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1253B ARG* 3.9 35.6 - - - +
1249D GLN 3.1 14.5 + - - +
1250D GLU* 3.0 15.8 + - - +
1252D ALA* 1.3 76.6 - - - +
1254D LYS* 1.3 59.3 + - - +
1255D MET 4.4 3.3 - - - -
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Residues in contact with LYS1254 (chain D).
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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1250D GLU* 2.9 15.3 + - + +
1251D THR* 3.5 13.7 - - - +
1252D ALA 3.1 0.4 - - - -
1253D ARG* 1.3 76.1 - - - +
1255D MET* 1.3 63.1 + - - +
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Residues in contact with MET1255 (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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1251D THR* 3.0 33.5 + - - +
1252D ALA* 3.1 32.7 + - + +
1253D ARG 4.4 3.1 - - - -
1254D LYS* 1.3 81.5 - - - +
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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