Contacts of the strand formed by residues 147 - 157 (chain B) 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 LEU 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B GLY* 2.7 30.7 + - - +
10B VAL 4.1 1.8 - - - +
11B LEU* 3.8 45.5 - - + +
104B PRO* 3.8 22.2 - - + -
145B ARG 4.1 0.2 - - - +
146B LEU* 1.3 83.7 - - - +
148B SER* 1.3 63.0 + - - +
360B TRP* 3.9 27.5 - - + -
361B MET 3.2 8.7 - - - +
362B VAL* 3.6 27.4 - - + +
363B SER* 4.5 1.3 - - - -
216D GLY* 6.2 0.2 - - - -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 1.3 77.0 - - - +
149B PRO* 1.3 75.2 - - - +
150B MET* 3.8 4.9 + - - +
279B ARG* 2.8 33.0 + - - -
360B TRP* 3.8 5.4 - - - -
361B MET* 3.0 29.0 + - - +
363B SER* 3.0 21.0 + - - -
216D GLY* 6.0 1.8 - - - -
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Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B SER* 1.3 87.8 - - - +
150B MET* 1.3 59.2 + - - +
279B ARG* 2.7 31.4 + - - +
357B ASN* 3.3 46.0 - - + +
359B PHE 3.4 8.1 - - - +
360B TRP* 3.6 26.2 - - + -
215D VAL* 5.2 3.1 - - + +
216D GLY* 3.7 26.5 - - - +
218D VAL 4.4 2.2 - - - +
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 4.1 17.9 - - - -
123B TYR* 4.7 2.0 - - + -
148B SER* 4.0 4.9 - - - +
149B PRO* 1.3 85.0 - - - +
151B ASN* 1.3 65.3 + - + +
264B LEU 5.4 1.1 - - - +
265B HIS* 2.9 37.0 - - + +
279B ARG* 3.7 25.6 - - + +
357B ASN* 3.9 3.8 - - - -
358B TYR 2.7 31.3 + - - -
359B PHE* 2.8 36.6 + - + +
361B MET* 3.6 34.3 - - + -
363B SER* 5.4 0.7 - - - -
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B MET* 1.3 84.0 - - + +
152B LEU* 1.3 59.8 + - - +
166B VAL 4.7 2.9 - - - +
264B LEU* 3.6 23.1 + - + +
265B HIS* 5.2 2.3 + - - -
280B CYS* 4.1 10.1 + - - +
281B ALA 3.0 25.1 + - - -
282B ALA* 3.4 4.6 - - - -
283B GLY 2.8 25.2 + - - -
284B VAL 3.2 15.4 + - - +
354B VAL* 3.7 12.8 - - + -
355B HIS 3.3 7.9 - - - +
356B PRO* 3.3 0.7 - - - +
357B ASN* 3.2 15.1 + - - +
359B PHE* 3.4 12.6 - - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B VAL* 4.1 7.9 - - + -
92B MET* 4.4 14.4 - - + -
101B ILE* 4.8 1.8 - - + -
150B MET 3.8 0.4 + - - -
151B ASN* 1.3 74.3 - - - +
153B LEU* 1.3 59.4 + - - +
154B SER 3.9 0.5 + - - -
164B PHE* 3.9 38.4 - - + -
165B SER 3.1 28.5 - - - +
166B VAL* 3.9 16.4 - - + -
264B LEU* 4.2 2.2 - - - -
354B VAL* 4.6 1.8 - - - -
355B HIS* 2.7 43.1 + - + +
358B TYR* 3.7 36.3 - - + -
359B PHE* 4.0 14.1 - - + -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 1.3 72.4 - - - +
154B SER* 1.3 74.4 + - - +
155B LEU* 3.8 20.8 + - + -
164B PHE* 3.2 8.0 - - - +
165B SER* 2.7 62.1 + - - +
169B LEU* 4.6 8.1 - - + +
262B ALA* 4.9 0.2 - - + -
264B LEU* 3.8 15.0 - - + +
285B MET* 3.7 36.3 - - + -
327B PHE* 4.1 5.8 - - + -
352B GLY* 3.8 7.9 - - - -
353B GLN 3.3 31.2 - - - +
354B VAL* 4.4 2.0 - - - +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU 3.9 0.6 + - - -
153B LEU* 1.3 70.6 - - - +
155B LEU* 1.3 60.0 + - - +
156B HIS* 4.3 0.5 - - - -
162B ARG* 2.8 33.3 + - - -
164B PHE* 3.4 16.7 - - - -
235B ASP* 2.9 29.5 + - - +
352B GLY* 3.0 25.1 - - - -
353B GLN 2.9 14.7 + - - -
355B HIS* 4.0 8.7 - - - -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.8 26.5 - - + +
154B SER* 1.3 71.1 + - - +
156B HIS* 1.3 67.6 + - - +
161B LEU 4.4 0.2 - - - -
162B ARG* 3.4 10.7 - - - +
163B LEU* 2.7 58.7 + - + +
165B SER* 4.2 9.6 - - - -
169B LEU* 3.9 16.8 - - + -
327B PHE* 4.0 13.5 - - + -
340B VAL* 3.9 29.4 - - + -
345B MET* 5.7 0.2 - - - -
350B VAL* 4.1 12.1 - - + -
351B GLN 3.4 13.5 - - - +
352B GLY* 4.0 8.3 - - - -
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Residues in contact with HIS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B SER 4.3 0.2 - - - -
155B LEU* 1.3 79.6 - - - +
157B THR* 1.3 63.7 + - - +
160B GLY* 6.3 0.7 - - - -
161B LEU 3.4 6.2 + - - +
162B ARG* 3.6 31.6 + - + +
235B ASP* 2.5 33.8 + - + +
238B LEU* 3.6 23.3 - - + +
241B LEU* 4.2 9.2 - - + +
350B VAL* 3.4 5.4 - - - +
351B GLN* 2.9 44.8 + - + +
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B HIS* 1.3 78.3 - - - +
158B ALA* 1.3 66.5 + - - +
159B SER* 3.6 9.4 + - - -
160B GLY* 3.1 13.0 + - - -
161B LEU* 2.9 40.4 + - + +
163B LEU* 4.0 22.0 - - + -
241B LEU* 3.2 13.7 - - - +
345B MET* 4.1 22.7 - - + -
347B SER* 3.5 14.4 + - - -
349B ALA 3.3 7.4 - - - -
350B VAL* 4.4 3.8 - - + -
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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