Contacts of the strand formed by residues 182 - 191 (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 PHE 182 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.6 32.8 - - + -
118A LEU* 3.9 29.2 - - + -
119A PHE 3.3 4.5 - - - -
120A LEU* 3.6 31.4 - - + -
147A PHE* 4.2 0.2 - - - -
180A THR* 3.7 2.4 + - - -
181A VAL* 1.3 82.2 - - - +
183A ALA* 1.3 66.9 + - - +
318A LEU* 4.0 17.5 - - + -
321A VAL* 5.0 6.3 - - + -
327A LEU* 4.0 21.3 - - + -
328A LYS 3.0 25.6 - - - +
329A LEU* 3.4 20.3 - - + +
330A SER* 2.8 30.2 + - - -
331A LYS 3.3 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY 3.4 2.6 - - - +
118A LEU* 3.6 1.6 - - - -
119A PHE* 2.7 53.0 + - + +
147A PHE* 4.3 9.4 - - + -
157A ILE* 4.4 13.2 - - + -
176A LEU* 4.8 2.9 - - + -
180A THR* 4.5 4.9 - - - +
182A PHE* 1.3 77.2 - - - +
184A LEU* 1.3 60.8 + - - +
185A VAL* 6.3 0.4 - - + -
329A LEU* 4.1 2.2 - - - -
331A LYS* 3.2 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 4.1 25.8 - - + +
61A PHE* 4.2 26.7 - - + -
63A MET* 5.0 0.7 - - + -
64A LEU* 4.7 8.5 - - + -
116A ASN* 3.9 13.7 - - - +
117A GLY 3.4 4.0 - - - +
118A LEU* 4.0 24.0 - - + -
183A ALA* 1.3 73.9 - - - +
185A VAL* 1.3 73.6 + - - +
186A ASN* 3.9 10.1 - - + +
299A LEU* 4.8 1.1 - - + -
329A LEU* 3.8 19.5 - - + +
331A LYS 2.7 11.1 + - - +
332A ALA* 3.2 9.3 - - + -
333A VAL* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 3.7 1.0 - - - +
116A ASN* 3.4 4.9 - - - +
117A GLY* 2.7 45.4 + - - +
119A PHE* 3.4 32.5 - - + -
157A ILE* 4.7 12.1 - - + -
160A TYR* 4.0 12.1 - - + -
161A VAL* 3.9 10.1 - - + -
172A LEU* 3.4 34.3 - - + -
173A VAL* 5.2 3.1 - - + -
183A ALA* 6.3 0.4 - - + -
184A LEU* 1.3 75.4 - - - +
186A ASN* 1.3 65.3 + - - +
187A TYR* 4.2 1.6 - - + -
333A VAL* 3.7 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 2.6 50.2 + - - +
57A ILE* 4.2 2.6 + - - -
60A ALA* 3.7 3.9 - - + +
114A THR* 5.2 1.2 + - - -
115A GLY 3.4 5.7 + - - -
116A ASN* 3.2 28.4 + - - +
184A LEU* 3.9 9.2 - - + -
185A VAL* 1.3 75.6 - - - +
187A TYR* 1.3 62.1 + - - +
299A LEU* 5.0 3.8 - - + -
333A VAL 2.8 15.8 + - - +
334A HIS* 2.8 27.7 + - - +
335A LYS* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 4.2 1.7 + - - -
113A THR* 4.6 3.1 - - + -
114A THR* 3.2 13.4 + - - -
115A GLY* 3.0 58.4 + - - +
141A GLU* 4.4 2.9 + - - -
160A TYR* 3.4 43.8 + + - -
161A VAL* 3.8 26.7 - - + -
164A GLY* 3.5 29.8 - - - -
165A THR* 3.4 26.2 - - + -
169A ILE* 4.1 14.1 - - + -
172A LEU* 5.0 2.2 - - + -
185A VAL* 4.6 4.5 - - + -
186A ASN* 1.3 76.4 - - - +
188A ILE* 1.3 62.0 + - - +
335A LYS* 3.3 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 3.9 19.7 - - - +
55A VAL* 6.6 0.4 - - + -
56A SER* 4.1 4.9 - - - +
112A LEU* 4.1 18.2 - - + -
113A THR 3.3 11.0 - - - +
114A THR* 3.7 19.3 - - + +
169A ILE* 4.7 3.0 - - - +
187A TYR* 1.3 76.9 - - - +
189A PHE* 1.3 62.9 + - - +
190A PHE 4.3 0.2 - - - -
334A HIS* 3.8 15.5 - - + -
335A LYS 2.9 8.8 + - - +
336A ALA* 3.4 24.3 - - + -
337A VAL* 2.8 28.3 + - - +
383A LEU* 5.1 2.9 - - + +
384A PHE* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 3.7 6.3 - - + +
112A LEU* 3.7 0.9 - - - -
113A THR* 2.8 48.7 + - - +
165A THR* 4.8 17.6 - - + +
168A LYS* 3.7 47.8 - - + -
188A ILE* 1.3 76.2 - - - +
190A PHE* 1.3 69.4 + - - +
191A LYS* 3.9 29.4 - - + -
337A VAL* 3.5 38.1 - - + -
339A THR* 3.9 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.8 26.0 - - + -
111A GLN 3.2 22.7 - - - -
112A LEU* 4.0 11.0 - - + -
189A PHE* 1.3 77.8 - - - +
191A LYS* 1.3 60.6 + - - +
192A GLY* 3.6 22.7 - - - -
244A TYR* 3.5 46.9 - + - -
248A ALA* 5.3 2.0 - - + -
337A VAL 2.9 11.7 + - - +
338A LEU* 3.4 19.5 - - + +
339A THR 3.1 22.4 + - - -
374A MET* 4.2 7.0 - - + -
383A LEU* 5.9 1.6 - - + -
384A PHE* 3.4 38.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 2.7 56.4 + - + +
168A LYS* 6.0 3.0 - - - +
189A PHE* 3.9 27.4 - - + -
190A PHE* 1.3 72.5 - - - +
192A GLY* 1.3 58.1 + - - +
339A THR* 3.7 31.4 - - + +
341A ASP* 3.3 24.7 - - - +
344A GLY* 3.5 26.5 + - - +
----------------------------------------------------------
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