Contacts of the strand formed by residues 331 - 340 (chain A) in PDB entry 3CWL
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 LYS 331 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 6.2 0.4 - - + -
173A VAL* 3.7 37.1 - - + +
174A LYS 5.3 1.4 - - - +
175A GLU* 3.2 22.4 + - - +
176A LEU* 3.6 22.9 - - + -
177A ASP 5.9 0.4 - - - +
180A THR* 4.7 3.6 - - - +
182A PHE 3.3 2.2 + - - -
183A ALA* 3.2 16.6 - - + -
184A LEU 2.7 32.2 + - - +
300A LYS* 5.6 1.8 - - - -
312A PHE* 5.3 0.2 - - - -
329A LEU* 3.5 6.9 - - - +
330A SER* 1.3 83.0 - - - +
332A ALA* 1.3 57.4 + - - +
333A VAL* 3.8 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.0 13.2 - - + -
184A LEU* 3.2 11.0 - - + +
298A ASP* 3.8 6.8 + - - +
299A LEU* 2.9 39.1 + - + -
300A LYS* 3.8 6.3 + - - +
312A PHE* 3.9 25.4 - - + -
329A LEU* 4.1 6.1 - - + -
331A LYS* 1.3 76.3 - - - +
333A VAL* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.1 28.5 - - + +
173A VAL* 4.8 6.3 - - + -
184A LEU* 3.0 9.6 + - - +
185A VAL* 4.7 8.1 - - + -
186A ASN* 2.8 35.2 + - - +
296A THR* 4.6 8.3 - - + -
297A TYR 3.5 11.9 - - - +
298A ASP* 5.4 3.1 - - - -
299A LEU* 4.1 4.9 - - - +
331A LYS* 3.8 34.3 - - + +
332A ALA* 1.3 79.8 - - - +
334A HIS* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.5 15.5 - - + -
53A SER* 3.0 29.9 + - - -
56A SER* 3.8 10.3 - - - -
57A ILE* 3.6 20.7 - - + +
186A ASN* 2.8 31.0 + - - -
188A ILE* 3.8 16.8 - - + -
295A GLY 3.7 0.7 - - - +
296A THR* 3.5 3.3 - - - -
297A TYR* 2.8 50.1 + + + +
299A LEU* 3.8 26.6 - - + +
333A VAL* 1.3 77.0 - - - +
335A LYS* 1.3 61.4 + - - +
336A ALA* 3.6 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.8 32.0 - - + +
170A VAL 5.7 1.6 + - - -
172A LEU* 3.6 38.7 - - + +
174A LYS* 6.1 0.8 - - - +
186A ASN 2.8 11.2 + - - +
187A TYR* 3.3 3.0 - - + +
188A ILE* 2.9 28.2 + - - +
294A THR* 4.1 26.1 + - - +
295A GLY 3.4 2.5 - - - +
296A THR* 3.3 29.5 + - - +
334A HIS* 1.3 76.6 - - - +
336A ALA* 1.3 59.8 + - - +
337A VAL* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.5 35.0 - - + +
52A PHE* 4.0 3.6 - - - -
53A SER 4.4 0.7 - - - +
188A ILE* 3.4 13.5 - - + -
294A THR* 3.0 8.3 - - - -
295A GLY 2.9 31.4 + - - +
334A HIS* 3.6 21.1 - - - +
335A LYS* 1.3 74.3 - - - +
337A VAL* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.6 5.0 - - - -
168A LYS* 5.2 5.8 - - + +
169A ILE* 3.8 34.5 - - + -
188A ILE 2.8 9.7 + - - +
189A PHE* 3.5 30.2 - - + -
190A PHE* 2.9 26.7 + - - +
292A SER* 4.6 10.5 - - - +
293A ILE 3.5 2.5 - - - +
294A THR* 3.7 23.1 - - + -
335A LYS* 4.3 8.7 - - - -
336A ALA* 1.3 78.3 - - - +
338A LEU* 1.3 63.4 + - - +
384A PHE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.3 26.2 - - + -
189A PHE* 5.2 0.2 - - - -
190A PHE* 3.4 37.2 - - + +
291A LEU* 3.8 1.5 - - + +
292A SER* 3.1 7.5 + - - -
293A ILE* 2.8 54.5 + - + +
337A VAL* 1.3 72.7 - - - +
339A THR* 1.3 73.7 + - - +
340A ILE* 4.1 26.9 - - + -
372A PHE* 3.7 33.2 - - + -
374A MET* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.9 17.9 - - - -
190A PHE 3.1 13.7 + - - +
191A LYS* 3.7 41.6 - - + +
192A GLY 4.0 7.1 + - - +
244A TYR* 5.1 0.9 + - - -
290A LYS* 6.1 0.2 - - + -
291A LEU 3.4 7.4 - - - +
292A SER* 3.6 14.6 + - - +
338A LEU* 1.3 81.4 - - - +
340A ILE* 1.3 73.1 + - - +
341A ASP* 4.2 7.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TRP* 3.9 19.3 - - + -
221A MET* 3.7 24.2 - - + -
244A TYR* 3.6 24.2 - - - +
252A PHE* 4.5 11.7 - - + -
288A LEU* 4.6 5.4 - - + -
289A PRO 3.9 7.0 - - - +
290A LYS* 3.3 8.1 - - - +
291A LEU* 2.7 60.1 + - + +
338A LEU* 4.1 13.2 - - + -
339A THR* 1.3 73.6 - - - +
341A ASP* 1.3 63.7 + - - +
374A MET* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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