Contacts of the strand formed by residues 301 - 305 (chain A) in PDB entry 3CL0
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 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A TYR 3.3 23.6 - - - +
275A TYR* 3.7 19.1 - - + -
290A VAL* 3.7 3.6 - - - +
291A CYS* 3.1 47.6 + - + +
293A ASP 3.7 15.9 - - - +
299A ASN 3.8 4.9 - - - +
300A ARG* 1.3 88.2 - - - +
302A TRP* 1.3 60.9 + - - +
315A GLY 3.3 8.5 - - - +
316A TYR* 3.6 25.5 - - + -
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Residues in contact with TRP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TYR* 2.6 25.3 + - - -
288A THR* 5.3 0.9 - - + -
289A CYS 3.1 14.4 - - - +
290A VAL* 4.6 2.2 - - + -
301A PRO* 1.3 74.7 - - - +
303A VAL* 1.3 61.8 + - - +
304A SER* 3.8 18.8 - - - -
313A GLN* 3.4 41.5 - - + -
314A ILE* 3.5 13.3 - - - -
315A GLY* 2.7 48.2 + - - -
316A TYR 3.4 29.6 + - - -
317A ILE* 3.7 8.0 - - + +
383A TRP* 3.5 53.1 + + + +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 5.1 6.7 - - + -
254A ILE* 4.3 7.4 - - + -
268A LEU* 4.0 20.2 - - + -
275A TYR* 3.4 30.5 - - + -
278A CYS* 5.1 2.0 - - - -
287A ILE 3.8 0.7 - - - +
288A THR* 3.6 1.0 - - - +
289A CYS* 2.8 45.4 + - + +
291A CYS* 4.6 1.1 - - - -
302A TRP* 1.3 74.0 - - - +
304A SER* 1.3 64.5 + - - +
305A PHE* 4.3 8.7 - - + -
312A TYR* 4.1 17.5 - - + -
313A GLN 3.5 11.0 - - - +
314A ILE* 3.8 14.1 - - + -
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Residues in contact with SER 304 (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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286A GLU* 4.1 14.3 + - - -
287A ILE 3.2 4.5 - - - -
288A THR* 3.0 29.7 + - - +
302A TRP* 3.8 16.2 - - - -
303A VAL* 1.3 74.3 + - - +
305A PHE* 1.3 62.1 + - - +
312A TYR* 3.2 2.3 - - - +
313A GLN* 2.9 42.6 + - - +
355A LYS* 5.7 3.8 - - - +
383A TRP* 5.6 0.5 - - - -
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Residues in contact with PHE 305 (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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238A PHE* 3.7 26.5 - + + -
239A THR* 5.9 0.2 - - - -
240A VAL* 4.7 5.2 - - + -
254A ILE* 3.7 42.6 - - + -
280A CYS* 5.7 0.2 - - + -
286A GLU* 3.8 9.8 - - - +
287A ILE* 3.0 70.7 + - + -
289A CYS* 3.7 26.2 - - - -
303A VAL* 4.3 9.4 - - + -
304A SER* 1.3 79.1 - - - +
306A ASN* 1.3 78.0 + - - +
310A LEU* 4.3 6.1 - - + -
311A GLU 3.2 10.8 - - - +
312A TYR* 3.8 11.0 - - + -
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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
------------------------------------------------------------
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