Contacts of the strand formed by residues 331 - 336 (chain B) in PDB entry 1M7X
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 ASN 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B ARG* 2.8 57.5 - - - +
236B ALA* 3.5 15.0 - - - +
237B ASN* 2.9 17.5 + - - -
282B THR 3.1 7.6 + - - +
283B HIS* 3.5 24.4 - - + +
284B LEU* 3.1 22.3 + - - +
329B GLY 5.4 1.2 + - - -
330B LEU* 1.3 78.9 - - - +
332B VAL* 1.3 65.7 + - - +
400B ASP* 3.6 15.3 - - + +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LEU* 3.4 16.2 - - + +
286B LEU* 4.1 22.7 - - + -
321B PHE* 5.4 1.8 - - + -
322B ILE* 4.3 18.6 - - + -
325B ALA* 3.7 28.0 - - + -
326B HIS* 4.2 11.7 - - + +
331B ASN* 1.3 81.6 - - - +
333B ILE* 1.3 74.8 + - - +
399B ILE* 3.9 14.1 - - + +
400B ASP* 3.0 34.7 + - - +
401B ALA 3.1 7.0 + - - +
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE* 3.5 38.8 - - + -
283B HIS* 3.7 26.5 - - + +
284B LEU 2.8 12.1 + - - +
285B GLU* 3.3 27.5 - - + +
286B LEU* 3.0 25.6 + - - +
332B VAL* 1.3 79.3 - - - +
334B LEU* 1.3 63.0 + - - +
401B ALA* 3.2 28.5 - - + +
402B LEU 4.5 0.4 - - - -
403B ARG* 4.0 18.2 - - + -
456B MET* 3.9 14.4 - - + -
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B LEU* 4.3 14.8 - - + +
289B ILE* 3.3 37.7 - - + +
332B VAL* 5.6 0.4 - - + -
333B ILE* 1.3 76.0 - - - +
335B ASP* 1.3 80.0 + - - +
336B TRP* 3.0 3.8 + - + +
393B TRP* 3.7 46.4 - - + +
399B ILE* 3.8 32.5 - - + -
401B ALA 2.7 9.7 + - - +
402B LEU* 3.4 9.4 - - + -
403B ARG 3.0 20.5 + - - -
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Residues in contact with ASP 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLU* 4.5 0.3 - - - +
285B GLU* 3.4 13.1 - - - +
286B LEU 3.0 24.3 + - - +
287B LEU* 3.9 8.7 - - - +
288B PRO* 3.5 35.7 - - + +
289B ILE 4.8 0.2 + - - -
290B ASN* 6.0 0.7 - - - -
300B TYR* 2.4 29.9 + - + +
333B ILE 4.2 0.2 + - - -
334B LEU* 1.3 78.5 - - - +
336B TRP* 1.3 59.4 + - - +
337B VAL* 4.2 0.3 + - - +
403B ARG* 2.6 45.1 + - - +
405B ASP* 5.8 0.4 - - - +
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Residues in contact with TRP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LEU* 5.1 5.1 - - + +
334B LEU* 3.0 9.6 + - + +
335B ASP* 1.3 73.6 - - - +
337B VAL* 1.3 66.2 + - - +
338B PRO* 3.1 39.0 - - + +
386B LEU* 3.2 29.6 - - + -
389B ASN* 2.9 26.8 + - + +
390B ALA* 3.8 21.2 - - + +
393B TRP* 4.3 15.5 - + - -
402B LEU* 3.8 29.4 - - + -
403B ARG 2.9 18.0 + - - +
404B VAL* 3.6 31.0 - - + -
405B ASP* 3.8 3.3 - - - +
438B PHE* 4.3 8.7 - + - -
439B LEU* 6.0 1.3 - - + -
442B THR* 4.0 26.0 - - + -
446B LEU* 5.6 0.9 - - + -
455B THR* 6.0 2.2 - - + -
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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