Contacts of the helix formed by residues 1233 - 1251 (chain A) in PDB entry 6FF7
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 ASP1233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A ASN* 5.6 6.5 - - + -
1191A GLY* 3.4 28.6 + - - +
1192A PHE* 4.0 3.5 - - - +
1193A GLU* 4.3 10.2 - - + +
1231A ARG 3.8 3.0 + - - -
1232A VAL* 1.3 77.3 - - - +
1234A ASP* 1.3 64.4 - - - +
1235A GLU* 4.3 9.0 - - + +
1236A SER* 3.3 13.6 + - - +
1237A MET* 3.5 10.2 + - - +
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Residues in contact with ASP1234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232A VAL 3.8 1.7 + - - -
1233A ASP* 1.3 72.4 - - - +
1235A GLU* 1.3 60.0 + - - +
1237A MET* 3.6 5.2 + - - +
1238A GLN* 2.9 30.3 + - - +
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Residues in contact with GLU1235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233A ASP* 3.2 5.5 - - + +
1234A ASP* 1.3 80.1 - - - +
1236A SER* 1.3 56.2 + - - +
1238A GLN* 3.8 6.9 - - - +
1239A ARG* 2.9 29.3 + - - +
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Residues in contact with SER1236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A GLY* 3.7 22.4 - - - -
1232A VAL* 5.3 5.8 - - - -
1233A ASP* 3.3 12.9 + - - +
1234A ASP 3.2 0.4 - - - -
1235A GLU* 1.3 76.8 - - - +
1237A MET* 1.3 61.5 + - - +
1239A ARG* 3.2 6.9 + - - +
1240A PHE* 2.9 27.9 + - - +
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Residues in contact with MET1237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232A VAL* 5.7 4.6 - - + +
1233A ASP 3.5 8.7 + - - +
1234A ASP* 4.3 6.5 - - - +
1236A SER* 1.3 75.0 - - - +
1238A GLN* 1.3 59.4 + - - +
1240A PHE* 3.4 7.0 + - - +
1241A HIS* 2.9 29.8 + - - +
1283A GLU 5.8 0.9 - - - +
1284A LEU* 4.6 22.9 - - + -
1287A LEU* 5.7 5.4 - - + -
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Residues in contact with GLN1238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234A ASP 2.9 20.2 + - - +
1235A GLU* 3.8 8.3 - - - +
1237A MET* 1.3 74.7 - - - +
1239A ARG* 1.3 60.0 + - - +
1241A HIS* 3.3 7.1 + - - +
1242A ASN* 2.9 29.6 + - - +
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Residues in contact with ARG1239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU 6.0 0.7 - - - -
1235A GLU 2.9 19.5 + - - +
1236A SER* 3.2 7.4 + - - +
1238A GLN* 1.3 76.1 - - - +
1240A PHE* 1.3 58.4 + - - +
1242A ASN* 3.5 5.5 + - - +
1243A ARG* 2.9 28.8 + - - +
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Residues in contact with PHE1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236A SER 2.9 15.6 + - - +
1237A MET* 3.9 7.0 - - - +
1238A GLN 3.3 0.2 - - - -
1239A ARG* 1.3 75.0 - - - +
1241A HIS* 1.3 60.2 + - - +
1243A ARG* 3.3 8.2 - - - +
1244A VAL* 2.9 29.8 + - - +
1270A LEU* 5.5 10.3 - - + -
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Residues in contact with HIS1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237A MET 2.9 18.6 + - - +
1238A GLN* 3.7 6.3 - - - +
1240A PHE* 1.3 76.5 - - - +
1242A ASN* 1.3 57.2 + - - +
1244A VAL* 3.5 4.5 + - - +
1245A ARG* 2.9 26.4 + - - +
1287A LEU* 6.0 6.3 - - + -
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Residues in contact with ASN1242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901A LEU* 4.0 10.1 - - - +
902A TYR* 3.7 33.2 - - + +
1238A GLN 2.9 17.5 + - - +
1239A ARG* 4.1 4.9 - - - +
1241A HIS* 1.3 74.1 - - - +
1243A ARG* 1.3 59.2 + - - +
1245A ARG* 3.2 9.2 + - - +
1246A GLN* 2.9 28.4 + - - +
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Residues in contact with ARG1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239A ARG 2.9 19.9 + - - +
1240A PHE* 3.3 11.0 - - - +
1242A ASN* 1.3 75.4 - - - +
1244A VAL* 1.3 58.1 + - - +
1246A GLN* 3.1 7.7 + - - +
1247A ILE* 3.0 24.5 + - - +
1266A ALA* 5.5 11.7 - - + -
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Residues in contact with VAL1244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A PHE 2.9 16.5 + - - +
1241A HIS* 4.2 4.0 - - - +
1243A ARG* 1.3 73.4 - - - +
1245A ARG* 1.3 59.0 + - - +
1247A ILE* 3.8 8.0 - - + +
1248A LEU* 2.9 28.1 + - - +
1291A CYS* 4.8 18.8 - - + -
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Residues in contact with ARG1245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241A HIS 2.9 16.3 + - - +
1242A ASN* 3.3 15.3 - - + +
1243A ARG 3.1 0.4 - - - -
1244A VAL* 1.3 78.1 - - - +
1246A GLN* 1.3 57.9 + - - +
1248A LEU* 3.2 8.5 + - - +
1249A MET* 3.0 24.4 + - - +
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Residues in contact with GLN1246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900A ASP 5.5 6.5 - - - +
1242A ASN 2.9 12.5 + - - +
1243A ARG* 3.1 7.1 + - - +
1245A ARG* 1.3 74.7 - - - +
1247A ILE* 1.3 61.0 + - - +
1249A MET* 3.6 8.8 - - + +
1250A ALA* 2.9 28.8 + - - +
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Residues in contact with ILE1247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243A ARG 3.0 14.6 + - - +
1244A VAL* 3.4 8.5 + - + +
1245A ARG 3.3 0.4 - - - -
1246A GLN* 1.3 76.2 - - - +
1248A LEU* 1.3 59.1 + - - +
1250A ALA* 3.4 7.0 + - - +
1251A SER* 2.9 27.0 + - - -
1259A ILE* 4.7 14.1 - - + +
1262A LYS* 4.9 17.0 - - + -
1263A TRP* 5.6 3.8 - - + +
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Residues in contact with LEU1248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405 U 4.8 11.8 + - - +
1244A VAL 2.9 14.2 + - - +
1245A ARG* 3.2 12.5 + - - +
1247A ILE* 1.3 75.2 - - - +
1249A MET* 1.3 64.1 + - - +
1251A SER* 3.4 18.8 - - - -
1252A GLY 4.4 1.2 + - - -
1298A ARG* 5.9 7.9 - - + -
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Residues in contact with MET1249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405 U 6.0 5.8 - - - -
767A VAL 5.6 5.4 - - - +
769A LYS* 6.4 2.5 - - + -
1245A ARG 3.0 13.4 + - - +
1246A GLN* 3.6 11.9 - - + +
1247A ILE 3.3 0.2 - - - -
1248A LEU* 1.3 78.7 - - - +
1250A ALA* 1.3 60.6 + - - +
1251A SER 3.2 1.1 + - - -
1252A GLY* 3.5 11.1 + - - -
1253A SER* 4.6 2.1 + - - -
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Residues in contact with ALA1250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246A GLN 2.9 16.8 + - - +
1247A ILE* 3.4 8.5 + - - +
1249A MET* 1.3 73.1 - - - +
1251A SER* 1.3 63.1 + - - +
1252A GLY 3.2 1.6 - - - -
1253A SER* 3.3 17.2 + - - +
1254A THR* 3.3 17.9 + - - -
1259A ILE* 5.8 1.1 - - - -
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Residues in contact with SER1251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247A ILE 2.9 13.3 + - - -
1248A LEU* 3.4 18.2 - - - -
1249A MET 3.2 0.8 - - - -
1250A ALA* 1.3 77.4 - - - +
1252A GLY* 1.3 56.6 + - - +
1254A THR* 3.0 23.8 - - - +
1255A THR 4.8 1.1 - - - +
1259A ILE* 4.8 15.9 - - - -
1298A ARG* 5.4 11.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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