Contacts of the helix formed by residues 1335 - 1343 (chain A) in PDB entry 6A5T
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 PHE1335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A ARG* 6.1 0.4 - - - -
1105A GLU 5.7 1.1 - - - -
1106A ILE* 4.5 22.2 - - + -
1109A VAL* 4.2 23.6 - - + -
1333A ASN 2.6 16.0 + - - +
1334A SER* 1.3 70.5 + - - +
1336A VAL* 1.3 65.7 + - + +
1337A GLU 3.1 2.0 - - - -
1338A ILE* 2.7 31.5 + - + +
1339A LEU* 2.9 8.7 + - - -
1347A THR* 3.9 22.1 + - + +
1350A SER* 3.9 23.3 - - - -
1351A LEU* 3.6 35.0 - - + -
1354A GLU* 4.9 9.2 - - + -
1384A LEU* 3.6 26.9 - - + -
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Residues in contact with VAL1336 (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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1109A VAL* 3.5 31.4 - - + -
1110A ALA 5.0 5.4 - - - +
1111A LYS* 4.8 31.9 - - + -
1334A SER* 3.4 4.1 - - - +
1335A PHE* 1.3 80.7 - - + +
1337A GLU* 1.3 58.5 + - - +
1339A LEU* 2.8 28.7 + - + +
1340A SER* 2.9 12.1 + - - -
1384A LEU* 3.6 16.4 - - + -
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Residues in contact with GLU1337 (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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1314A ILE* 2.9 41.3 - - + +
1315A ASN* 3.3 5.9 + - - -
1316A LEU* 2.5 44.9 + - + +
1332A SER* 4.4 5.2 + - - -
1334A SER* 3.4 12.4 + - - +
1335A PHE 3.1 0.4 - - - -
1336A VAL* 1.3 78.8 - - - +
1338A ILE* 1.3 57.8 + - + +
1340A SER* 2.5 30.7 + - - +
1341A VAL* 2.9 15.0 + - + +
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Residues in contact with ILE1338 (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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1316A LEU* 3.5 29.4 - - + -
1330A THR 5.8 0.2 - - - +
1331A TYR* 5.7 1.8 - - + -
1332A SER* 4.1 26.7 - - - +
1335A PHE* 2.7 32.3 + - + +
1337A GLU* 1.3 70.0 - - + +
1339A LEU* 1.3 61.3 + - - +
1341A VAL* 4.8 0.4 - - - -
1342A LEU* 2.8 39.8 + - + +
1343A GLY 3.5 4.2 - - - +
1346A ALA* 3.8 21.1 - - + +
1347A THR* 3.4 26.0 - - - +
1350A SER* 4.2 11.4 - - - +
148E LEU* 6.0 1.8 - - + -
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Residues in contact with LEU1339 (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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1335A PHE 2.9 5.6 + - - +
1336A VAL* 2.8 23.8 + - + +
1338A ILE* 1.3 78.1 - - - +
1340A SER* 1.3 63.9 + - - +
1343A GLY* 3.2 30.3 + - - +
1344A ILE* 3.6 23.8 - - + -
1347A THR* 2.9 18.9 + - + +
1382A GLY 3.9 13.0 - - - +
1383A TYR* 4.6 10.8 - - + -
1384A LEU* 4.6 12.6 - - + +
178E GLN* 5.0 9.6 - - - +
181E ASP* 3.8 12.9 - - - +
182E PRO* 4.4 2.3 - - - +
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Residues in contact with SER1340 (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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1336A VAL 2.9 9.8 + - - -
1337A GLU* 2.5 28.2 + - - +
1339A LEU* 1.3 79.0 - - - +
1341A VAL* 1.3 66.6 + - - +
182E PRO* 3.3 22.7 - - - +
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Residues in contact with VAL1341 (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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1316A LEU* 4.2 28.9 - - + -
1317A ALA* 4.6 19.5 - - + +
1320A MET* 4.7 6.1 - - - -
1337A GLU* 2.9 13.6 + - + +
1338A ILE 4.4 0.2 - - - +
1340A SER* 1.3 90.7 + - - +
1342A LEU* 1.3 80.2 + - + +
1343A GLY 3.1 9.0 + - - -
143E ILE* 5.2 7.5 - - + +
182E PRO* 3.2 22.3 - - - +
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Residues in contact with LEU1342 (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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1316A LEU* 4.2 18.6 - - + -
1320A MET* 4.1 13.5 - - + -
1330A THR 4.7 4.0 - - - +
1338A ILE* 2.8 24.8 + - + +
1341A VAL* 1.3 90.2 - - + +
1343A GLY* 1.3 64.3 + - - +
1344A ILE 3.7 0.3 + - - -
1346A ALA* 3.5 20.4 + - + +
143E ILE* 3.9 29.8 - - + -
146E HIS* 4.2 32.5 - - + +
148E LEU* 5.1 2.7 - - + -
149E VAL* 3.0 29.0 - - + +
182E PRO* 5.3 0.2 - - - -
183E VAL* 5.2 2.0 - - - -
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Residues in contact with GLY1343 (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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1338A ILE 3.5 1.3 + - - +
1339A LEU* 3.2 13.8 + - - +
1341A VAL 3.1 9.1 + - - -
1342A LEU* 1.3 81.1 - - - +
1344A ILE* 1.3 59.6 + - - -
1347A THR* 2.9 19.9 + - - -
149E VAL* 6.1 0.2 - - - -
181E ASP* 3.2 22.7 - - - -
182E PRO* 4.4 6.6 - - - +
183E VAL* 4.6 13.0 - - - -
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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