Contacts of the helix formed by residues 244 - 248 (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 PRO 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.9 7.0 - - + +
79A GLY* 3.7 9.2 - - - -
80A HIS 3.4 39.0 - - - +
81A PHE* 3.4 24.5 - - + -
242A VAL 3.7 0.4 - - - -
243A PRO* 1.3 90.7 - - + +
245A PRO* 1.3 77.0 - - + +
246A GLN* 3.1 13.2 + - - +
247A VAL* 3.2 14.5 + - + +
248A ARG* 2.9 2.5 + - - +
1205B GLN* 4.1 18.4 - - - +
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Residues in contact with PRO 245 (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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54A ASN* 4.9 11.2 - - - +
58A LEU* 3.9 17.9 - - + +
59A GLY 3.2 27.4 - - - +
60A SER* 5.3 0.2 - - - -
61A ILE* 4.1 22.2 - - + -
244A PRO* 1.3 85.3 - - + +
246A GLN* 1.3 62.7 + - - +
247A VAL 3.2 0.4 - - - -
248A ARG* 2.8 23.7 + - + +
249A PRO* 2.8 33.7 - - + +
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Residues in contact with GLN 246 (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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58A LEU 4.9 0.2 - - - +
59A GLY* 4.9 8.5 + - - -
60A SER 4.8 11.1 + - - -
61A ILE* 4.8 11.0 - - + +
74A MET* 5.9 4.0 + - - +
77A CYS* 3.4 23.2 + - - +
78A PRO 3.7 13.6 - - - +
79A GLY* 3.5 20.1 - - - +
244A PRO* 3.1 10.3 + - + +
245A PRO* 1.3 79.6 - - - +
247A VAL* 1.3 59.1 + - + +
249A PRO* 3.0 24.0 - - - +
1113B VAL 5.4 1.0 - - - +
1114B LEU* 3.8 10.4 - - - +
1198B TYR* 3.9 23.6 + - + +
1201B LYS* 5.1 1.3 - - - +
1202B LEU* 4.9 2.7 - - + +
1205B GLN* 4.9 6.3 - - - +
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Residues in contact with VAL 247 (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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243A PRO* 4.0 20.4 - - + -
244A PRO* 3.2 12.4 + - + +
245A PRO 3.2 0.6 - - - -
246A GLN* 1.3 75.9 - - - +
248A ARG* 1.3 59.8 + - - +
249A PRO* 3.4 4.0 - - - +
261A ASP* 4.1 0.7 - - - +
263A LEU* 3.8 20.0 - - + -
326A ILE* 6.1 1.1 - - + -
329A ARG* 3.7 15.9 + - - +
1114B LEU* 3.9 6.6 - - - +
1202B LEU* 4.0 17.7 - - + -
1205B GLN* 3.5 38.6 - - + +
1206B GLU* 4.0 25.4 - - + +
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Residues in contact with ARG 248 (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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53A LEU* 2.7 35.2 + - - +
54A ASN* 3.9 5.4 + - - -
58A LEU* 4.6 8.5 - - - +
242A VAL* 4.7 9.2 - - - +
243A PRO* 2.1 42.3 + - - +
244A PRO 2.9 20.2 + - - -
245A PRO* 2.8 17.9 + - + +
247A VAL* 1.3 82.9 - - + +
249A PRO* 1.3 66.2 - - - +
250A SER* 3.1 3.1 + - - -
260A GLN* 5.2 0.2 - - - +
261A ASP* 3.0 31.9 - - + +
263A LEU* 3.7 27.8 - - + -
264A THR* 3.2 28.1 + - - +
267A LEU* 4.5 5.9 - - - +
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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