Contacts of the helix formed by residues 251 - 261 (chain A) in PDB entry 3MAP
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 ILE 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A SER* 3.2 46.0 - - - +
211A THR* 2.9 31.1 + - - +
212A LYS* 3.9 18.2 - - + +
249A ARG 3.4 1.0 + - - -
250A LEU* 1.3 70.0 - - - +
252A ASP* 1.3 64.4 + - - +
254A MET* 3.5 0.7 - - - +
255A VAL* 2.9 48.5 + - + +
267A TRP* 5.7 0.9 - - + -
269A CYS* 5.1 4.9 - - - -
270A LYS 4.4 15.0 - - - +
271A ASN* 6.3 0.2 - - - +
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Residues in contact with ASP 252 (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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212A LYS* 5.7 5.1 - - - +
214A THR* 5.4 0.9 + - - -
250A LEU* 2.7 23.7 + - + +
251A ILE* 1.3 78.2 + - - +
253A ASP* 1.3 69.4 + - - +
254A MET 3.0 1.3 - - - -
255A VAL* 3.1 26.2 - - - +
256A ALA* 3.2 9.1 + - - +
281B VAL* 4.7 13.0 + - - -
424B ICT 5.5 4.1 + - - -
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Residues in contact with ASP 253 (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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249A ARG* 4.4 16.3 - - + +
250A LEU* 2.9 33.7 + - - +
252A ASP* 1.3 76.8 - - - +
254A MET* 1.3 56.8 + - - +
256A ALA* 3.8 6.4 - - - +
257A GLN* 2.9 29.1 + - - +
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Residues in contact with MET 254 (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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208A TYR* 3.7 33.2 - - + -
210A SER* 3.5 9.6 - - - -
249A ARG* 3.7 21.9 - - + +
250A LEU 2.7 16.0 + - - +
251A ILE 3.5 4.3 - - - +
253A ASP* 1.3 75.4 - - - +
255A VAL* 1.3 59.9 + - - +
256A ALA 3.1 1.1 - - - -
257A GLN* 3.1 7.3 + - + +
258A ALA* 2.9 28.8 + - + +
265A PHE* 3.3 39.3 - - + -
267A TRP* 3.4 40.4 - - + +
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Residues in contact with VAL 255 (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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251A ILE* 2.9 26.5 + - + +
252A ASP* 3.1 20.2 - - - +
254A MET* 1.3 75.5 - - - +
256A ALA* 1.3 63.8 + - + +
258A ALA* 3.6 0.4 + - - -
259A MET* 3.1 36.0 + - + +
267A TRP* 3.8 26.9 - - + -
281B VAL* 6.2 4.7 - - - -
283B GLN* 4.7 19.5 - - + -
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Residues in contact with ALA 256 (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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252A ASP 3.2 12.7 + - - +
253A ASP* 3.8 7.9 - - - +
254A MET 3.1 0.4 - - - -
255A VAL* 1.3 81.2 - - + +
257A GLN* 1.3 64.9 + - - +
259A MET* 3.5 7.3 + - - +
260A LYS* 3.1 28.1 + - + +
423B NAP 5.9 2.5 - - - +
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Residues in contact with GLN 257 (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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208A TYR* 4.1 19.9 + - + +
249A ARG* 3.3 42.7 - - - +
253A ASP 2.9 19.1 + - - +
254A MET* 3.1 10.3 + - + +
256A ALA* 1.3 74.3 - - - +
258A ALA* 1.3 54.1 + - - +
260A LYS* 3.1 12.3 + - - +
261A SER* 2.7 39.8 + - - -
265A PHE* 5.9 0.7 - - + -
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Residues in contact with ALA 258 (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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124A TRP* 2.7 31.0 + - + -
128A ILE* 5.9 0.2 - - + -
254A MET 2.9 15.0 + - - +
255A VAL 3.8 1.1 - - - +
256A ALA 3.3 0.2 - - - -
257A GLN* 1.3 76.2 - - - +
259A MET* 1.3 74.3 + - + +
261A SER* 2.8 21.2 + - - +
265A PHE* 3.8 26.9 - - + -
267A TRP* 3.9 13.5 - - + -
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Residues in contact with MET 259 (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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120A LEU* 3.9 16.4 - - + -
121A VAL* 3.5 44.6 - - + +
124A TRP* 3.3 29.8 - - + -
255A VAL* 3.1 24.2 + - + +
256A ALA* 3.9 7.2 - - - +
257A GLN 3.4 0.4 - - - -
258A ALA* 1.3 83.8 - - + +
260A LYS* 1.3 62.3 + - + +
261A SER 3.4 2.1 + - - +
267A TRP* 5.2 4.7 - - + -
283B GLN* 4.9 18.6 - - + +
284B GLY 5.6 3.4 - - - +
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Residues in contact with LYS 260 (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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256A ALA* 3.1 20.9 + - + +
257A GLN* 3.1 14.6 + - - +
259A MET* 1.3 76.8 - - + +
261A SER* 1.3 57.4 + - - +
262A GLU* 5.6 1.2 - - - +
314B ARG* 4.0 14.5 - - - +
423B NAP 2.8 53.4 + - - -
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Residues in contact with SER 261 (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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121A VAL* 4.7 0.3 - - - +
123A GLY* 4.0 4.9 - - - +
124A TRP* 3.0 10.7 + - - -
257A GLN* 2.7 29.2 + - - -
258A ALA* 2.8 19.4 + - - +
259A MET 3.8 4.7 - - - +
260A LYS* 1.3 80.2 - - - +
262A GLU* 1.3 69.1 + - - +
263A GLY* 3.0 21.8 + - - -
265A PHE* 4.1 9.4 - - - -
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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