Contacts of the strand formed by residues 333 - 337 (chain A) in PDB entry 3C5E
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 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A THR* 3.2 23.6 - - - +
250A GLY* 3.5 22.8 + - - -
251A LEU* 4.4 0.8 - - - +
255A ASP* 5.3 0.6 + - - -
306A LYS* 3.0 11.3 + - - +
307A SER* 2.9 27.3 + - - +
308A MET* 2.8 32.4 + - - +
331A LEU* 4.0 1.4 - - - +
332A GLN* 1.3 91.8 + - - +
334A CYS* 1.3 59.9 + - - +
335A VAL* 5.3 1.6 - - + -
374A LYS* 2.7 39.8 + - + +
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Residues in contact with CYS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 3.5 9.6 - - - -
315A TYR* 3.4 17.3 - - + +
331A LEU* 3.7 27.1 - - - -
332A GLN 4.2 0.4 + - - -
333A ASN* 1.3 77.6 - - - +
335A VAL* 1.3 62.8 + - - +
349A TRP* 3.6 27.6 - - - +
355A LEU* 3.8 11.9 - - - -
356A ASP 3.5 16.5 + - - +
357A ILE* 3.3 4.3 - - - -
358A ARG* 2.8 25.6 + - - +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP* 3.8 24.9 - - + -
249A THR* 4.1 36.3 - - + +
257A MET* 4.4 1.8 - - + -
308A MET 2.9 19.7 + - - +
309A MET* 3.5 29.3 - - + -
310A GLY 3.3 14.0 + - - -
315A TYR* 2.8 16.8 + - - -
333A ASN 5.3 0.9 - - - -
334A CYS* 1.3 79.4 - - - +
336A THR* 1.3 62.5 + - - +
357A ILE* 4.3 0.7 - - - -
358A ARG* 3.1 22.0 - - + +
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Residues in contact with THR 336 (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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309A MET* 3.7 5.8 - - - -
310A GLY 2.7 20.3 + - - -
311A ALA 3.4 0.5 - - - -
312A PRO* 3.1 26.1 - - + +
315A TYR* 3.9 10.3 - - - -
335A VAL* 1.3 75.7 - - - +
337A VAL* 1.3 65.1 + - - +
339A GLU 5.4 0.2 - - - +
341A LEU* 4.2 15.3 - - + -
357A ILE* 3.8 13.9 - - + -
358A ARG 3.0 5.7 + - - -
359A GLU* 3.8 28.0 - - + -
360A SER* 2.8 31.8 + - - -
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Residues in contact with VAL 337 (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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267A LEU* 3.8 38.5 - - + +
309A MET* 4.0 8.7 - - + -
310A GLY 3.8 2.6 + - - -
311A ALA* 3.6 11.3 - - - +
312A PRO* 3.5 15.8 - - - +
336A THR* 1.3 74.0 + - - +
338A GLY* 1.3 69.4 + - - +
339A GLU 3.7 3.6 - - - -
360A SER* 3.2 39.9 - - - +
361A TYR* 3.9 9.6 - - - +
368A LEU* 5.8 0.4 - - + -
801A ATP 4.1 4.0 - - - +
805A UNL 4.6 5.4 - - + -
806A UNL 4.2 20.0 - - + -
807A UNL 4.2 0.4 - - + -
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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