Contacts of the strand formed by residues 350 - 362 (chain A) in PDB entry 3VZC
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 VAL 350 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.1 22.9 - - + -
156A HIS 3.2 10.8 - - - +
157A THR* 4.4 3.4 - - + -
169A LEU* 4.1 13.2 - - + -
241A LEU* 4.4 2.2 - - - -
327A PHE* 4.2 8.2 - - + -
328A ARG* 3.5 1.4 - - - +
329A LEU* 2.8 33.3 + - - +
338A PHE* 3.7 29.8 - - + -
345A MET* 3.6 28.9 - - + -
347A SER* 4.0 3.4 - - - -
349A ALA* 1.3 81.1 - - - +
351A GLN* 1.3 71.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.3 5.2 - - - +
156A HIS* 2.9 45.2 + - + +
238A LEU* 4.1 26.9 - - + +
239A VAL 2.8 23.2 + - - +
240A PRO* 4.4 0.7 - - - +
241A LEU* 3.7 23.6 + - + +
249A TRP* 4.7 4.6 - - - -
327A PHE* 3.2 16.2 - - - +
328A ARG* 2.9 40.2 - - + +
350A VAL* 1.3 80.5 - - - +
352A GLY* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 4.0 5.4 - - - -
154A SER 2.9 15.3 - - - -
155A LEU* 4.1 8.1 - - - -
238A LEU* 3.6 10.5 - - - +
326A ALA* 3.1 5.9 - - - +
327A PHE* 3.0 38.3 + - - +
351A GLN* 1.3 77.2 - - - +
353A GLN* 1.3 60.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.7 6.1 - - - -
154A SER* 3.0 29.9 + - - +
235A ASP* 3.0 35.7 - - + +
236A ALA* 4.2 5.7 - - - +
237A HIS* 2.8 48.3 + - + +
238A LEU* 3.8 6.5 + - + +
285A MET* 6.0 0.2 - - - -
325A VAL 3.2 13.2 - - - +
326A ALA* 3.8 10.3 - - + +
352A GLY* 1.3 74.6 - - - +
354A VAL* 1.3 69.9 + - - +
355A HIS* 3.7 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 3.6 31.0 - - + -
152A LEU 3.5 8.5 - - - +
153A LEU* 4.6 2.0 - - + +
237A HIS* 5.5 1.2 + - - -
264A LEU* 5.1 1.8 - - + -
283A GLY* 3.5 32.7 - - - +
284A VAL 4.1 3.1 - - - +
285A MET* 3.5 47.8 - - + +
325A VAL* 2.9 17.7 + - - +
353A GLN* 1.3 85.1 + - - +
355A HIS* 1.3 65.2 + - - +
356A PRO* 4.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 3.4 4.5 - - - +
152A LEU* 2.8 39.3 + - + +
154A SER* 3.7 19.4 - - - -
164A PHE* 5.2 2.7 - + - -
233A PRO* 4.0 20.1 - - + +
234A VAL 3.3 19.5 - - - -
235A ASP* 2.6 30.5 + - - -
353A GLN* 3.7 20.8 + - - +
354A VAL* 1.3 72.8 - - - +
356A PRO* 1.3 70.8 - - - +
358A TYR* 3.6 37.7 + + + +
215E VAL* 6.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 3.2 8.1 - - - +
282A ALA* 3.9 5.2 - - + -
283A GLY* 3.5 15.0 - - - +
354A VAL 4.2 4.7 - - - +
355A HIS* 1.3 85.8 - - + +
357A ASN* 1.3 73.2 + - + +
358A TYR* 2.9 19.2 + - + -
215E VAL* 4.9 10.8 - - + +
281E ALA* 3.5 32.8 - - + -
284E VAL* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 3.6 44.1 - - + +
150A MET* 3.3 12.6 + - - -
151A ASN* 3.0 17.2 + - - +
282A ALA* 3.6 25.5 - - - +
356A PRO* 1.3 71.7 - - + +
358A TYR* 1.3 62.3 + - - +
359A PHE 3.6 0.7 - - - -
360A TRP* 5.0 4.7 + - - -
277E MET* 4.2 18.6 - - - +
278E GLY 4.8 2.6 - - - +
279E ARG 5.5 0.2 + - - -
286E HIS* 5.4 2.6 + - - -
321E TYR* 5.2 4.0 + - - +
323E PRO* 5.3 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A MET* 4.5 7.2 - - + -
97A TRP* 4.0 15.8 - + - -
101A ILE* 3.7 26.6 - - + +
102A GLN* 5.2 4.5 + - - +
150A MET 2.8 10.0 + - - +
152A LEU* 3.9 37.9 - - + -
233A PRO* 3.2 41.9 - - + +
355A HIS* 3.6 27.0 + + + +
356A PRO* 3.3 16.4 - - + -
357A ASN* 1.3 76.3 - - - +
359A PHE* 1.3 58.6 + - - +
360A TRP* 4.9 3.7 + - - -
215E VAL* 4.1 26.5 + - + +
216E GLY* 3.9 19.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 5.3 2.2 - - - -
88A VAL* 4.7 4.9 - - + -
101A ILE* 3.5 31.6 - - + +
105A LEU* 3.7 25.8 - - + -
116A LEU* 5.4 1.1 - - + -
149A PRO* 3.3 3.3 - - - +
150A MET* 2.8 49.0 + - + -
151A ASN 3.4 22.9 - - - -
152A LEU* 4.1 17.3 - - + -
166A VAL* 4.0 32.5 - - + -
265A HIS* 5.5 0.9 - - - -
358A TYR* 1.3 76.4 - - - +
360A TRP* 1.3 63.6 + - - +
361A MET* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.2 48.0 - - - -
9A GLY* 4.0 3.4 - - - -
101A ILE 4.3 2.8 + - - -
102A GLN* 4.3 33.2 - - + +
103A LYS 4.0 2.2 + - - +
104A PRO* 3.5 15.2 - - + +
105A LEU* 2.9 25.1 + - - +
147A LEU* 3.9 25.8 - - + -
148A SER 3.5 3.8 - - - -
149A PRO* 4.0 27.8 - - + +
357A ASN 5.0 4.4 + - - -
358A TYR 4.9 2.0 + - - -
359A PHE* 1.3 86.1 - - - +
361A MET* 1.3 67.2 + - - +
312E MET* 4.9 0.2 - - + -
321E TYR* 4.2 32.3 - + + -
323E PRO* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 4.5 10.3 - - - -
105A LEU* 3.1 17.0 - - + +
107A SER* 5.0 2.0 - - - -
116A LEU* 3.8 35.7 - - + -
120A LEU* 3.7 26.0 - - + -
147A LEU* 3.3 7.4 - - - -
148A SER 2.8 31.8 + - - +
150A MET* 3.4 36.1 - - + -
265A HIS* 4.6 0.7 - - + -
359A PHE* 3.4 26.5 - - + -
360A TRP* 1.3 79.3 - - - +
362A VAL* 1.3 65.9 + - - +
363A SER* 3.5 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.3 16.4 - - + -
74A ALA* 5.3 3.1 - - + -
104A PRO* 5.3 0.2 - - + -
105A LEU 3.0 8.4 + - - +
106A CYS* 3.5 36.7 - - + +
107A SER 5.7 0.4 + - - +
120A LEU* 3.9 17.2 - - - +
138A CYS 4.7 0.9 - - - +
141A LEU* 3.8 10.0 - - + +
142A LEU* 3.6 35.9 - - + +
145A ARG 5.3 0.9 - - - -
146A LEU 3.1 12.6 - - - +
147A LEU* 3.7 13.5 - - + -
361A MET* 1.3 69.7 - - - +
363A SER* 1.3 65.7 + - - +
----------------------------------------------------------
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