Contacts of the strand formed by residues 338 - 345 (chain A) in PDB entry 3C0M
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ARG* 3.3 22.0 + - - +
320A GLY 3.3 10.5 - - - +
321A PHE* 3.1 24.0 + - - +
336A ARG 4.6 0.7 - - - -
337A PRO* 1.3 71.8 - - - +
339A TRP* 1.3 62.1 + - - +
340A ASN* 4.1 2.1 + - - +
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Residues in contact with TRP 339 (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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125A TYR* 4.4 9.9 - - - +
319A SER* 3.4 3.3 - - - -
320A GLY 2.9 28.9 + - - +
322A LEU* 3.2 34.5 - - + -
329A TRP* 3.2 65.0 - + - -
331A THR* 5.1 1.8 - - + -
333A PRO* 4.2 10.5 - - + -
337A PRO* 3.2 40.9 + - + -
338A ASN* 1.3 75.3 - - - +
340A ASN* 1.3 84.0 + - - +
341A HIS* 4.2 9.3 + - + +
371A TRP* 4.6 2.7 - + - -
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Residues in contact with ASN 340 (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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317A THR* 4.5 12.6 - - - +
318A LEU 3.6 3.4 - - - -
319A SER* 2.7 30.8 + - - -
338A ASN 5.0 2.5 - - - +
339A TRP* 1.3 84.8 - - - +
341A HIS* 1.3 59.8 + - - +
342A THR* 5.1 5.2 - - - +
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Residues in contact with HIS 341 (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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125A TYR* 3.4 6.6 + - - +
316A LEU 3.9 0.2 - - - +
317A THR* 3.3 3.7 - - - +
318A LEU* 2.6 43.6 + - + +
329A TRP* 4.2 12.4 - + - -
339A TRP* 4.5 4.4 + - + -
340A ASN* 1.3 76.2 + - - +
342A THR* 1.3 89.2 + - + +
343A PHE* 3.8 17.5 - + + -
352A ALA* 3.1 32.8 + - + -
370A TRP* 4.5 14.1 - + - -
371A TRP* 3.5 46.3 + + + -
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Residues in contact with THR 342 (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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315A ASP* 4.2 13.5 + - - +
316A LEU 3.0 6.6 + - - -
317A THR* 3.2 26.2 + - + +
340A ASN* 5.1 4.0 - - - +
341A HIS* 1.3 96.9 + - + +
343A PHE* 1.3 65.5 + - - +
344A VAL* 5.0 2.6 - - - +
353A SER* 3.8 11.4 - - - -
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Residues in contact with PHE 343 (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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119A LEU* 4.4 11.9 - - + -
123A LEU* 3.7 24.7 - - + -
315A ASP* 3.7 1.7 - - - -
316A LEU* 2.7 39.8 + - + +
318A LEU* 4.2 17.3 - - + -
341A HIS* 3.8 17.3 - + - -
342A THR* 1.3 77.9 + - - +
344A VAL* 1.3 61.9 + - - +
345A ILE* 3.9 9.2 - - + -
352A ALA 4.5 0.9 - - - -
353A SER 3.5 15.9 - - - +
355A ILE* 3.3 39.0 - - + -
358A GLN* 4.2 5.6 - - - -
371A TRP* 3.3 38.6 - + - -
373A TRP* 4.1 12.1 - + - -
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Residues in contact with VAL 344 (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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313A SER* 6.2 0.9 - - - -
314A TYR 4.0 4.5 - - - +
315A ASP* 4.1 24.7 - - - +
342A THR* 5.0 2.7 - - - +
343A PHE* 1.3 75.8 - - - +
345A ILE* 1.3 64.3 + - - +
346A GLY* 3.3 14.4 + - - +
347A PRO* 4.0 21.5 - - + +
349A LYS* 4.2 27.8 - - + +
353A SER* 2.9 41.2 + - - +
354A SER* 5.2 2.3 - - - -
355A ILE 5.4 1.2 + - - -
393A LEU* 5.6 1.7 - - - +
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Residues in contact with ILE 345 (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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312A VAL 4.6 1.5 - - - +
313A SER* 3.4 6.9 - - - -
314A TYR* 2.9 73.3 + - + +
316A LEU* 4.1 28.0 - - + -
343A PHE* 4.5 11.2 - - + -
344A VAL* 1.3 77.2 - - - +
346A GLY* 1.3 57.4 + - - +
355A ILE* 4.5 3.4 - - + -
392A VAL* 4.1 20.9 - - + +
393A LEU* 4.1 28.9 - - + +
394A ARG 5.3 4.9 - - - +
396A VAL* 6.5 0.2 - - + -
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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