Contacts of the strand formed by residues 147 - 157 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F SER 4.2 4.7 - - - +
9F GLY* 2.8 30.1 + - - +
10F VAL 3.6 30.3 - - - +
11F LEU* 3.6 34.3 - - + -
104F PRO* 4.1 22.4 - - + -
145F ARG 4.0 1.8 - - - +
146F LEU* 1.3 82.5 - - - +
148F SER* 1.3 65.4 + - - +
149F PRO* 4.6 0.2 - - - +
360F TRP* 3.8 18.8 - - + -
361F MET 3.2 8.5 - - - +
362F VAL* 3.8 21.8 - - + +
363F SER* 4.0 0.7 - - - -
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Residues in contact with SER 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU* 1.3 74.6 + - - +
149F PRO* 1.3 73.3 - - - +
150F MET* 3.6 5.5 - - - +
279F ARG* 3.8 27.2 + - - -
360F TRP* 3.7 4.5 - - - -
361F MET 2.8 30.4 + - - +
363F SER* 2.7 24.6 + - - -
364F GLY 5.3 3.5 + - - -
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Residues in contact with PRO 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F MET* 6.1 1.8 - - - -
147F LEU 4.6 0.2 - - - +
148F SER* 1.3 91.9 - - - +
150F MET* 1.3 68.6 + - - +
279F ARG* 4.2 5.0 + - - -
357F ASN* 3.4 46.6 - - + +
359F PHE 3.3 9.0 - - - +
360F TRP* 3.6 30.0 - - + -
1002F EDO 4.5 2.3 + - - -
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Residues in contact with MET 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LEU* 4.4 17.7 - - + -
123F TYR* 4.6 4.7 - - + -
148F SER* 3.6 14.8 - - - +
149F PRO* 1.3 89.5 - - - +
151F ASN* 1.3 60.0 + - - +
265F HIS* 2.7 41.3 - - + +
279F ARG* 4.1 11.7 - - - -
357F ASN* 3.8 3.8 - - - +
358F TYR 2.7 29.3 + - - -
359F PHE* 2.8 34.8 + - + +
361F MET* 3.8 24.7 - - + -
1002F EDO 3.1 25.1 - - - +
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Residues in contact with ASN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F MET* 1.3 73.4 - - - +
152F LEU* 1.3 61.2 + - - +
166F VAL 4.5 3.8 - - - +
264F LEU* 3.8 18.0 + - + +
265F HIS* 5.0 2.1 + - - -
280F CYS* 4.3 0.4 - - - +
281F ALA 3.2 24.0 + - - -
282F ALA* 3.5 4.7 - - - +
283F GLY 2.9 21.7 + - - +
284F VAL 3.4 14.5 + - - -
354F VAL* 3.6 17.5 - - + -
355F HIS 3.4 4.0 - - - +
356F PRO* 3.5 0.7 - - - +
357F ASN* 3.0 18.3 + - - +
359F PHE* 3.3 17.2 - - - -
1002F EDO 2.8 32.6 + - - +
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Residues in contact with LEU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F VAL* 3.8 15.5 - - + -
92F MET* 4.8 4.5 - - + -
101F ILE* 5.4 1.3 - - + -
150F MET 3.9 0.2 + - - -
151F ASN* 1.3 75.5 - - - +
153F LEU* 1.3 63.0 + - - +
154F SER* 3.8 1.8 + - - +
164F PHE* 3.3 41.1 - - + -
165F SER 3.4 21.1 - - - +
166F VAL* 3.8 14.1 - - + -
233F PRO* 6.1 0.2 - - + -
264F LEU* 4.2 2.2 - - - -
354F VAL* 4.5 0.7 - - - -
355F HIS* 2.8 40.2 + - + +
358F TYR* 3.7 34.5 - - + -
359F PHE* 3.6 24.2 - - + -
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Residues in contact with LEU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 1.3 73.4 - - - +
154F SER* 1.3 81.2 + - - +
155F LEU* 3.8 19.1 - - + -
164F PHE* 3.2 8.7 - - - +
165F SER* 2.8 61.7 + - - +
169F LEU* 4.6 10.5 - - + +
262F ALA* 4.7 0.2 - - + -
264F LEU* 3.7 12.7 - - + +
285F MET* 3.6 33.9 - - + -
327F PHE* 4.0 15.5 - - + -
352F GLY 3.9 3.6 - - - -
353F GLN* 3.7 19.7 - - - +
354F VAL* 4.5 2.2 - - - +
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Residues in contact with SER 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 3.8 0.6 + - - -
153F LEU* 1.3 73.4 - - - +
155F LEU* 1.3 59.9 + - - +
156F HIS* 4.3 0.3 + - - -
162F ARG* 2.6 38.0 + - - -
164F PHE* 3.5 14.7 - - - -
235F ASP* 2.9 25.0 + - - +
351F GLN 3.9 0.2 - - - +
352F GLY* 2.8 26.2 - - - -
353F GLN 3.0 15.2 + - - -
355F HIS* 3.8 9.0 - - - -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LEU* 3.8 18.8 - - + +
154F SER* 1.3 74.9 + - - +
156F HIS* 1.3 62.4 + - - +
162F ARG* 3.3 9.7 - - - +
163F LEU* 2.7 60.9 + - + +
165F SER* 4.1 15.3 - - - +
169F LEU* 4.0 23.8 - - + -
327F PHE* 3.7 29.8 - - + -
340F VAL* 4.0 19.1 - - + -
345F MET* 6.3 0.4 - - - -
350F VAL* 3.9 19.3 - - + -
351F GLN 3.5 5.2 - - - +
352F GLY* 4.2 0.2 - - - -
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Residues in contact with HIS 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F SER* 4.4 1.6 - - - -
155F LEU* 1.3 81.7 - - - +
157F THR* 1.3 66.3 + - - +
160F GLY 6.0 0.6 + - - -
161F LEU 3.4 5.5 + - - +
162F ARG* 3.7 30.0 + - + +
235F ASP* 2.8 32.3 + - + +
238F LEU* 4.0 15.0 - - + -
241F LEU* 4.4 6.4 - - + +
349F ALA 3.8 0.3 - - - +
350F VAL* 3.3 7.1 - - - +
351F GLN* 2.8 44.5 + - + +
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Residues in contact with THR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F HIS* 1.3 79.4 - - - +
158F ALA* 1.3 57.8 + - - +
159F SER* 3.2 10.6 + - - -
160F GLY* 2.7 25.3 + - - -
161F LEU* 2.9 38.8 + - + +
163F LEU* 4.5 14.1 - - + -
241F LEU* 3.5 10.2 - - - +
345F MET* 4.1 14.8 - - + -
347F SER* 3.6 17.0 - - - +
349F ALA 3.2 4.9 - - - -
350F VAL* 3.8 22.0 - - + -
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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