Contacts of the strand formed by residues 350 - 362 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 4.0 26.7 - - + -
156E HIS 3.4 12.6 - - - +
157E THR* 4.2 6.1 - - + -
169E LEU* 4.5 16.6 - - + -
241E LEU* 4.4 2.5 - - - -
327E PHE* 4.1 3.4 - - + -
328E ARG* 3.5 0.3 - - - -
329E LEU* 2.7 45.7 + - + +
338E PHE* 3.5 35.4 - - + -
345E MET* 4.0 12.6 - - + -
347E SER* 3.9 10.5 - - - +
349E ALA* 1.3 80.6 - - - +
351E GLN* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 3.5 8.5 - - - +
156E HIS* 2.9 46.0 + - + +
238E LEU* 3.7 32.2 - - + +
239E VAL* 2.6 33.2 + - - +
240E PRO* 4.0 6.1 - - - +
241E LEU* 3.4 26.4 - - + +
249E TRP* 4.5 4.9 - - - -
327E PHE* 3.3 12.6 - - - +
328E ARG* 3.4 24.7 - - + +
350E VAL* 1.3 76.1 - - - +
352E GLY* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E LEU* 3.8 12.8 - - - -
154E SER 3.0 13.5 - - - -
155E LEU* 4.1 4.0 - - - -
238E LEU* 3.9 8.7 - - - +
326E ALA* 3.1 8.0 - - - +
327E PHE* 3.0 37.5 + - - +
351E GLN* 1.3 75.1 - - - +
353E GLN* 1.3 60.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E LEU* 3.6 4.7 - - - +
154E SER* 2.8 34.3 + - - +
234E VAL 4.0 1.2 + - - -
235E ASP* 3.0 28.8 - - - +
236E ALA* 3.7 12.5 - - - +
237E HIS* 2.9 55.2 + - + +
238E LEU* 3.9 8.0 + - + +
325E VAL 3.4 6.7 - - - +
326E ALA* 4.6 1.1 - - + -
352E GLY* 1.3 73.5 - - - +
354E VAL* 1.3 72.8 + - - +
355E HIS* 3.6 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ASN* 3.8 26.7 - - + -
152E LEU 3.7 8.5 - - - +
153E LEU* 4.5 1.8 - - - +
237E HIS* 5.9 0.5 - - - -
264E LEU* 4.8 4.7 - - + -
283E GLY 4.0 17.2 - - - +
284E VAL 4.0 12.6 - - - +
285E MET* 3.3 41.3 - - + +
324E VAL 3.8 1.8 - - - +
325E VAL* 2.8 27.7 + - - +
353E GLN* 1.3 85.3 + - - +
355E HIS* 1.3 64.6 + - - +
356E PRO* 4.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY 5.4 2.0 + - - +
151E ASN* 3.4 5.4 - - - +
152E LEU* 2.8 38.6 + - + +
154E SER* 3.7 12.0 - - - -
164E PHE* 5.9 0.7 - + - -
233E PRO* 4.3 16.4 - - + +
234E VAL 3.5 20.0 - - - -
235E ASP* 2.6 28.2 + - - -
353E GLN* 3.6 30.7 + - - +
354E VAL* 1.3 76.3 + - - +
356E PRO* 1.4 69.2 - - + +
358E TYR* 3.7 34.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL 4.1 8.3 - - - +
219A GLY* 3.1 37.1 - - - +
221A LYS* 4.1 21.8 - - - +
151E ASN* 3.2 9.4 - - - +
282E ALA* 4.1 11.0 - - + -
283E GLY* 3.5 22.6 - - - +
354E VAL 4.0 6.1 - - - +
355E HIS* 1.4 89.4 - - + +
357E ASN* 1.3 69.7 + - - +
358E TYR* 3.0 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 2.7 67.2 + - - +
218A VAL* 3.7 11.6 + - - +
219A GLY* 3.6 12.0 + - - -
149E PRO* 3.5 34.1 - - + +
150E MET 3.4 8.3 + - - -
151E ASN* 3.1 11.6 + - - +
282E ALA* 3.7 17.5 - - - +
356E PRO* 1.3 71.8 - - - +
358E TYR* 1.3 60.4 + - - +
359E PHE 3.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY* 4.5 15.3 - - - -
92E MET* 3.9 21.3 - - + -
97E TRP* 3.1 26.2 - + - -
101E ILE* 3.8 33.5 - - + +
102E GLN* 5.3 3.8 - - - +
150E MET 2.8 7.6 + - - +
152E LEU* 3.9 32.8 - - + -
233E PRO* 3.3 18.4 - - + +
355E HIS* 3.7 33.7 - - + +
356E PRO 3.9 9.2 - - - +
357E ASN* 1.3 74.4 - - - +
359E PHE* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E MET* 5.5 1.8 - - - -
88E VAL* 4.9 2.2 - - + -
101E ILE* 3.3 29.8 - - + +
102E GLN* 5.4 1.1 - - - +
105E LEU* 3.7 21.5 - - + -
116E LEU* 6.0 0.2 - - + -
149E PRO* 3.3 5.1 - - - +
150E MET* 2.9 47.0 + - + -
151E ASN 3.4 24.2 - - - -
152E LEU* 4.1 25.1 - - + -
166E VAL* 4.0 22.0 - - + -
265E HIS* 5.7 0.9 - - - -
357E ASN 3.5 0.8 - - - -
358E TYR* 1.3 83.2 - - - +
360E TRP* 1.3 74.7 + - - +
361E MET* 3.4 29.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 360 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLY* 5.9 6.5 - - - -
218A VAL* 6.3 3.1 - - + -
8E SER* 4.1 19.5 - - - -
9E GLY* 4.4 6.5 - - - -
101E ILE 4.5 2.4 + - - -
102E GLN* 3.2 36.2 + - + +
103E LYS 4.3 2.0 + - - +
104E PRO* 4.0 19.6 - - + +
105E LEU* 3.1 18.3 + - - +
147E LEU* 3.6 40.6 - - + -
148E SER 3.8 16.8 - - - -
149E PRO* 3.7 26.2 - - + -
359E PHE* 1.3 87.8 - - - +
361E MET* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E MET* 4.6 6.5 - - + -
105E LEU* 3.0 24.9 - - + +
106E CYS* 4.1 3.4 - - - -
107E SER 4.5 7.6 - - - -
116E LEU* 3.8 40.4 - - + -
120E LEU* 3.8 17.0 - - + -
147E LEU* 3.3 7.3 - - - -
148E SER 3.0 32.5 + - - +
150E MET* 3.4 26.7 - - + -
359E PHE* 3.4 30.9 + - + -
360E TRP* 1.3 72.8 - - - +
362E VAL* 1.3 69.9 + - - +
363E SER* 3.9 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 4.4 7.0 - - + -
74E ALA* 5.4 3.4 - - + -
104E PRO* 5.5 0.2 - - + -
105E LEU 2.9 16.6 + - - +
106E CYS* 3.8 25.7 - - + -
120E LEU* 3.9 17.3 - - - +
138E CYS 4.9 0.7 - - - +
141E LEU* 3.8 13.3 - - + +
142E LEU* 3.7 45.3 - - + +
145E ARG 5.4 0.2 - - - -
146E LEU 3.3 13.2 - - - +
147E LEU* 4.0 14.1 - - + -
361E MET* 1.3 74.2 - - - +
363E SER* 1.3 63.7 + - - +
----------------------------------------------------------
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