Contacts of the strand formed by residues 146 - 157 (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 LEU 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A MET* 5.9 1.1 - - + -
7A GLY* 4.5 8.5 - - - +
9A GLY 3.5 2.5 - - - +
10A VAL* 3.7 17.9 - - + -
141A LEU 4.5 2.2 + - - +
144A ARG* 3.3 18.1 - - + +
145A ARG* 1.3 78.3 - - - +
147A LEU* 1.3 61.3 + - - +
362A VAL* 3.1 9.2 - - - +
363A SER 2.9 37.9 + - - +
364A GLY* 4.3 17.7 - - - -
313E GLU* 3.6 48.9 - - + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 3.6 2.3 - - - -
8A SER* 2.7 32.6 + - - -
9A GLY* 2.8 18.6 + - - +
10A VAL 3.5 32.5 - - - +
11A LEU* 3.7 17.9 - - + +
104A PRO* 3.8 29.6 - - + -
145A ARG 3.8 6.3 - - - +
146A LEU* 1.3 86.3 - - - +
148A SER* 1.3 55.5 + - - +
360A TRP* 3.9 17.9 - - + -
361A MET 3.3 4.0 - - - +
362A VAL* 3.7 22.9 - - + +
363A SER 4.5 1.6 - - - -
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 4.2 14.6 + - - +
7A GLY* 4.7 0.5 - - - -
8A SER* 4.6 1.1 - - - -
147A LEU* 1.3 73.7 + - - +
149A PRO* 1.4 69.8 - - - +
150A MET* 3.9 6.1 + - - +
279A ARG* 4.0 27.2 + - - -
360A TRP* 3.5 4.7 - - - -
361A MET* 2.8 29.9 + - - +
363A SER* 3.2 26.4 + - - -
364A GLY 5.5 1.0 + - - -
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 3.7 22.2 - - - +
148A SER* 1.4 86.0 - - - +
150A MET* 1.3 74.6 + - - +
279A ARG* 4.2 2.8 + - - +
357A ASN* 3.6 43.7 - - + +
359A PHE 3.3 9.0 - - - +
360A TRP* 4.0 24.7 - - + -
277E MET* 4.1 15.9 - - + -
321E TYR* 6.1 0.9 - - + -
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.3 11.4 - - - -
123A TYR* 5.0 0.7 - - + -
148A SER* 4.0 14.8 - - - +
149A PRO* 1.3 94.3 - - - +
151A ASN* 1.3 61.6 + - - +
265A HIS* 3.9 24.0 - - + -
279A ARG* 2.9 32.1 - - - +
357A ASN* 3.7 5.8 - - - -
358A TYR 2.8 27.7 + - - -
359A PHE* 2.8 37.7 + - + +
361A MET* 3.4 40.6 - - + -
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Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A MET* 1.3 80.0 - - - +
152A LEU* 1.3 57.7 - - - +
166A VAL 4.7 2.4 - - - +
264A LEU* 3.5 24.4 + - + +
265A HIS* 5.0 3.0 + - - -
280A CYS* 4.2 9.7 + - - +
281A ALA 3.0 25.7 + - - -
282A ALA* 4.2 0.4 - - - +
283A GLY 2.9 22.0 + - - -
284A VAL 3.3 13.9 + - - +
354A VAL* 3.6 17.0 - - + -
355A HIS 3.4 3.8 - - - -
356A PRO* 3.2 1.0 - - - +
357A ASN* 3.0 22.0 + - - +
359A PHE* 3.4 13.3 - - - -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 3.8 22.7 - - + -
92A MET* 4.0 26.5 - - + -
101A ILE* 5.0 3.4 - - + -
150A MET 3.9 0.6 + - - -
151A ASN* 1.3 74.1 - - - +
153A LEU* 1.3 61.4 + - - +
154A SER 3.9 0.5 + - - -
164A PHE* 3.8 34.5 - - + -
165A SER 3.3 22.7 - - - +
166A VAL* 4.0 6.1 - - + -
264A LEU* 4.0 3.4 - - - -
354A VAL* 3.5 3.7 - - - -
355A HIS* 2.8 37.2 + - + +
358A TYR* 3.9 26.4 - - + +
359A PHE* 4.1 13.9 - - + -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 1.3 73.1 - - - +
154A SER* 1.3 79.8 + - - +
155A LEU* 3.6 25.3 + - + -
164A PHE* 3.2 9.7 - - - +
165A SER* 2.8 63.6 + - - +
169A LEU* 4.6 11.2 - - + +
264A LEU* 3.8 8.9 - - + +
285A MET* 3.5 34.8 - - + -
327A PHE* 4.4 7.0 - - + -
352A GLY* 4.0 3.1 - - - -
353A GLN* 3.4 24.2 - - - +
354A VAL* 4.3 2.5 - - + +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU 3.9 1.4 + - - -
153A LEU* 1.3 72.8 - - - +
155A LEU* 1.3 59.3 + - - +
156A HIS* 4.1 0.2 + - - -
162A ARG* 2.8 31.8 + - - -
163A LEU 3.7 4.3 - - - -
164A PHE* 3.9 7.9 - - - -
235A ASP* 2.8 31.1 + - - +
352A GLY* 2.9 24.8 - - - -
353A GLN 3.0 14.5 + - - -
355A HIS* 3.7 15.9 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.6 27.1 - - + -
154A SER* 1.3 77.9 + - - +
156A HIS* 1.3 63.2 + - - +
162A ARG* 3.3 9.0 - - - +
163A LEU* 2.9 54.7 + - + +
165A SER* 3.9 24.2 - - - -
169A LEU* 4.3 16.2 - - + -
327A PHE* 3.8 23.3 - - + -
340A VAL* 4.0 19.1 - - + -
345A MET* 5.6 0.2 - - - -
350A VAL* 4.1 11.7 - - + -
351A GLN 3.3 8.5 - - - +
352A GLY* 4.1 0.2 - - - -
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Residues in contact with HIS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER* 4.4 0.2 - - - -
155A LEU* 1.3 77.2 - - - +
157A THR* 1.3 64.4 + - - +
160A GLY 5.8 1.4 + - - -
161A LEU 3.4 6.6 + - - +
162A ARG* 3.4 30.7 - - + +
235A ASP* 2.5 35.0 + - + +
238A LEU* 3.6 21.9 - - + +
241A LEU* 4.4 6.3 - - + +
349A ALA 3.9 0.2 - - - +
350A VAL* 3.2 7.4 - - - +
351A GLN* 2.9 44.3 + - + +
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A HIS* 1.3 81.3 - - - +
158A ALA* 1.3 55.9 + - - +
159A SER* 3.3 18.6 + - - -
160A GLY* 2.7 28.3 + - - -
161A LEU* 3.1 27.5 + - + +
163A LEU* 4.1 11.7 - - + -
241A LEU* 3.7 7.0 - - - +
345A MET* 3.9 33.7 - - + -
347A SER* 3.5 13.7 - - - -
349A ALA 3.2 5.2 - - - -
350A VAL* 4.4 4.3 - - + -
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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