Contacts of the strand formed by residues 350 - 362 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D LEU* 4.0 29.4 - - + -
156D HIS 3.2 12.3 - - - +
157D THR* 4.7 2.2 - - + -
169D LEU* 4.4 17.9 - - + -
241D LEU* 4.4 2.5 - - - -
327D PHE* 4.3 2.6 - - + -
328D ARG* 3.5 0.7 - - - +
329D LEU* 2.9 32.3 + - + +
338D PHE* 3.7 28.9 - - + -
345D MET* 3.7 28.3 - - + -
347D SER* 4.5 4.3 - - - -
349D ALA* 1.3 82.3 - - - +
351D GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 3.4 5.7 - - - +
156D HIS* 2.9 41.9 + - + +
238D LEU* 4.2 26.1 - - + +
239D VAL 2.9 21.9 + - - +
240D PRO* 4.1 1.0 - - - +
241D LEU* 3.6 25.7 + - + +
249D TRP* 4.9 3.2 - - - -
327D PHE* 3.2 16.8 - - - +
328D ARG* 2.8 42.6 - - + +
350D VAL* 1.3 80.3 - - - +
352D GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LEU* 3.9 11.9 - - - -
154D SER 2.9 14.6 - - - -
155D LEU* 4.1 0.9 - - - -
238D LEU* 3.7 10.4 - - - +
326D ALA* 3.1 5.9 - - - +
327D PHE* 2.9 40.5 + - - +
351D GLN* 1.3 77.2 - - - +
353D GLN* 1.3 61.0 + - - -
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Residues in contact with GLN 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LEU* 3.4 7.3 - - - +
154D SER* 2.9 30.5 + - - +
234D VAL 4.5 0.4 + - - -
235D ASP* 3.0 34.7 - - - +
236D ALA* 4.1 7.7 - - - +
237D HIS* 2.9 50.4 + - + +
238D LEU* 3.8 7.7 + - + +
325D VAL 3.1 11.9 - - - +
326D ALA* 3.9 9.0 - - + +
352D GLY* 1.3 74.6 - - - +
354D VAL* 1.3 70.3 + - - +
355D HIS* 3.7 15.6 + - - +
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ASN* 3.6 23.6 - - + -
152D LEU 3.5 7.9 - - - +
153D LEU* 4.5 3.6 - - + +
237D HIS* 5.4 1.7 + - - -
264D LEU* 5.2 1.6 - - + -
283D GLY* 3.5 38.0 - - - +
284D VAL 4.0 2.7 - - - +
285D MET* 3.5 45.1 - - + +
325D VAL* 2.8 21.3 + - - +
353D GLN* 1.3 90.9 + - - +
355D HIS* 1.3 63.6 + - - +
356D PRO* 4.1 4.9 - - - +
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Residues in contact with HIS 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ASN* 3.4 2.8 - - - -
152D LEU* 2.8 34.4 + - + +
154D SER* 3.8 19.2 - - - -
164D PHE* 5.5 2.5 - + - -
233D PRO* 3.9 20.4 - - + +
234D VAL 3.3 19.3 - - - -
235D ASP* 2.4 30.0 + - - -
353D GLN* 3.7 16.0 + - - +
354D VAL* 1.3 80.3 + - - +
356D PRO* 1.3 72.2 - - - +
358D TYR* 3.6 39.7 + + + -
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Residues in contact with PRO 356 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B VAL* 5.1 10.1 - - + +
281B ALA* 3.4 33.7 - - + -
284B VAL* 4.6 13.2 - - + -
151D ASN* 3.3 8.7 - - - +
282D ALA* 3.8 7.4 - - + -
283D GLY* 3.6 16.4 - - - +
354D VAL 4.1 4.5 - - - +
355D HIS* 1.3 86.2 - - + +
357D ASN* 1.3 73.7 + - + +
358D TYR* 2.9 15.6 + - + -
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Residues in contact with ASN 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B MET* 4.3 22.0 - - - +
278B GLY 5.1 2.4 - - - +
286B HIS* 5.6 2.2 + - - -
321B TYR* 5.2 4.4 + - - -
323B PRO* 5.2 13.7 - - + +
149D PRO* 3.4 36.2 - - + +
150D MET* 3.2 13.6 + - - -
151D ASN* 3.0 17.0 + - - +
282D ALA* 3.7 24.5 - - - +
355D HIS 3.6 0.2 + - - -
356D PRO* 1.3 72.5 - - + +
358D TYR* 1.3 64.7 + - - +
359D PHE 3.5 1.3 + - - -
360D TRP* 5.8 2.1 + - - -
1002D EDO 5.5 0.3 + - - -
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Residues in contact with TYR 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B VAL* 3.9 25.5 + - + +
216B GLY* 3.9 20.2 - - - -
92D MET* 4.6 6.1 - - + -
97D TRP* 3.8 21.7 - + - -
101D ILE* 3.7 28.9 - - + +
102D GLN* 4.9 6.4 + - - +
150D MET 2.8 9.7 + - - -
152D LEU* 4.0 38.4 - - + -
233D PRO* 3.4 30.0 - - + +
355D HIS* 3.6 31.3 + - + +
356D PRO* 2.9 16.3 + - + -
357D ASN* 1.3 77.9 - - - +
359D PHE* 1.3 56.9 + - - +
360D TRP* 5.5 0.8 - - - -
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Residues in contact with PHE 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D MET* 5.4 2.0 - - - -
88D VAL* 4.6 4.7 - - + -
101D ILE* 3.2 33.2 - - + +
105D LEU* 3.7 25.6 - - + -
116D LEU* 5.7 0.7 - - + -
149D PRO* 3.2 3.1 - - - +
150D MET* 2.7 49.4 + - + -
151D ASN 3.5 21.5 - - - -
152D LEU* 4.2 22.0 - - + -
166D VAL* 4.1 27.1 - - + -
265D HIS* 5.7 0.7 - - - -
357D ASN 3.5 0.2 - - - -
358D TYR* 1.3 78.0 - - + +
360D TRP* 1.3 69.3 + - - +
361D MET* 3.4 32.8 - - + -
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Residues in contact with TRP 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B MET* 4.6 1.1 - - + -
312B MET* 5.0 0.2 - - + -
321B TYR* 4.1 29.4 - + + -
323B PRO* 6.3 0.7 - - + -
8D SER* 3.2 47.3 - - - -
9D GLY* 3.9 2.0 - - - -
101D ILE 4.3 2.2 + - - -
102D GLN* 4.0 35.1 + - + +
103D LYS 4.2 1.5 + - - +
104D PRO* 3.6 15.4 - - + +
105D LEU* 3.0 22.3 + - - +
147D LEU* 3.7 29.2 - - + -
148D SER 3.6 4.0 - - - -
149D PRO* 3.6 35.1 - - + +
357D ASN 5.8 1.6 + - - -
358D TYR 5.5 1.1 - - - -
359D PHE* 1.3 83.6 - - - +
361D MET* 1.3 66.0 + - - +
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Residues in contact with MET 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D MET* 4.2 15.7 - - - -
105D LEU* 3.1 11.0 - - + +
107D SER* 4.9 3.1 - - - -
116D LEU* 3.7 36.8 - - + -
120D LEU* 3.7 34.8 - - + -
147D LEU* 3.2 7.3 - - - -
148D SER 2.8 37.0 + - - +
150D MET* 3.7 24.9 - - + -
265D HIS* 4.6 1.1 - - + -
359D PHE* 3.4 30.1 - - + -
360D TRP* 1.3 74.1 - - - +
362D VAL* 1.3 68.3 + - - +
363D SER* 3.5 1.2 + - - -
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.3 17.3 - - + -
74D ALA* 5.3 2.2 - - + -
104D PRO* 5.2 1.1 - - + -
105D LEU 2.9 17.6 + - - +
106D CYS* 3.6 35.8 - - + -
107D SER 5.5 0.6 + - - +
120D LEU* 3.9 14.6 - - - +
138D CYS 5.0 0.7 - - - +
141D LEU* 4.1 9.5 - - + +
142D LEU* 3.8 28.5 - - + +
145D ARG 5.2 1.8 - - - -
146D LEU 3.1 10.8 - - - +
147D LEU* 3.8 14.6 - - + -
361D MET* 1.3 74.1 - - - +
363D SER* 1.3 63.8 + - - +
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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
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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