Contacts of the helix formed by residues 337 - 349 (chain V) in PDB entry 1MVW
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 TYR 337 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410G ASN* 4.9 5.6 - - + -
18V LYS* 3.8 21.1 - - + -
26V ALA* 4.5 11.0 - - + -
27V PRO* 3.6 43.1 - - + -
30V VAL* 4.1 18.1 - - + +
334V GLU 2.8 12.1 + - - +
336V LYS* 1.3 124.6 + - + +
338V SER* 1.4 62.5 + - - -
339V VAL* 3.3 3.8 - - - -
340V TRP* 3.0 8.8 + - + +
341V ILE* 2.9 38.6 + - + +
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Residues in contact with SER 338 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636G LYS 5.2 0.9 - - - -
637G LYS* 4.9 5.1 + - - +
140V LEU 3.8 0.3 - - - +
141V SER* 3.2 28.5 + - - -
144V ALA* 3.5 11.4 - - - +
298V VAL* 5.9 0.3 - - - +
299V MET 4.4 2.4 + - - -
300V SER* 3.7 15.6 - - - -
332V PRO* 5.2 6.1 - - - +
334V GLU* 3.8 7.4 + - - -
335V ARG* 3.3 25.2 + - - +
336V LYS 3.8 0.2 - - - -
337V TYR* 1.4 73.0 - - - +
339V VAL* 1.3 55.8 + - - +
341V ILE* 3.1 8.4 + - - -
342V GLY* 2.8 31.9 + - - -
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Residues in contact with VAL 339 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V ASP* 3.4 34.1 - - + +
106V THR* 4.2 2.2 - - + -
137V GLN* 4.0 25.4 - - + +
140V LEU* 3.3 27.0 - - + +
141V SER* 3.1 24.2 - - - +
154V ASP* 4.2 17.0 - - - +
300V SER* 4.5 3.8 - - - +
337V TYR 5.0 1.1 - - - -
338V SER* 1.3 82.5 - - - +
340V TRP* 1.3 61.1 + - - +
343V GLY 3.2 14.4 + - - -
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Residues in contact with TRP 340 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642G LYS* 2.5 70.2 + - + -
9V VAL* 2.8 43.5 + - + +
11V ASP* 4.0 9.2 - - + +
18V LYS* 3.4 39.7 + - + -
19V ALA* 3.6 6.4 - - - +
20V GLY* 3.6 27.1 - - - -
21V PHE 3.5 10.3 - - - -
24V ASP* 3.8 3.6 - - + -
25V ASP 4.3 0.4 - - - -
26V ALA* 3.5 27.8 - - - -
27V PRO* 3.7 16.8 - - + -
106V THR* 6.2 0.2 - - - -
337V TYR* 3.0 18.7 + - + +
339V VAL* 1.3 78.1 - - - +
341V ILE* 1.3 61.4 + - + +
343V GLY* 3.0 3.5 + - - -
344V SER 2.9 12.1 + - - -
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Residues in contact with ILE 341 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633G GLY* 5.5 2.9 - - - -
635G GLY* 2.7 65.1 - - - +
636G LYS 3.2 14.4 - - - +
637G LYS 3.4 8.7 - - - -
638G GLY* 2.0 35.3 - - - -
639G GLY 4.9 0.9 - - - +
642G LYS* 2.9 16.3 + - - +
25V ASP 3.5 15.7 - - - +
26V ALA* 5.6 0.2 - - + -
334V GLU* 3.7 17.0 - - + +
337V TYR* 2.9 35.7 + - + +
338V SER 3.6 4.0 - - - +
340V TRP* 1.3 80.1 - - + +
342V GLY* 1.3 52.2 + - - +
345V ILE 3.0 2.6 + - - -
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Residues in contact with GLY 342 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637G LYS 4.0 0.4 - - - -
638G GLY* 3.7 4.0 - - - -
140V LEU* 3.4 31.4 - - - +
143V TYR* 3.7 7.7 - - - -
144V ALA* 3.5 12.9 - - - +
338V SER 2.8 10.9 + - - -
339V VAL 3.8 0.9 - - - -
341V ILE* 1.3 77.0 - - - +
343V GLY* 1.3 53.9 + - - +
345V ILE* 3.7 0.3 + - - +
346V LEU* 3.1 29.6 + - - +
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Residues in contact with GLY 343 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V VAL* 3.9 15.7 - - - -
104V LEU* 4.3 7.0 - - - +
140V LEU* 3.8 18.6 - - - +
339V VAL 3.2 7.9 + - - -
340V TRP 3.0 7.8 + - - -
342V GLY* 1.3 76.3 - - - +
344V SER* 1.3 54.0 + - - +
346V LEU* 3.8 2.4 - - - +
347V ALA* 2.8 38.5 + - - +
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Residues in contact with SER 344 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639G GLY* 2.4 26.5 + - - -
642G LYS* 0.7 192.0 - - - +
9V VAL* 3.9 6.4 - - - +
22V ALA* 3.7 0.7 - - - +
23V GLY 3.7 1.2 + - - -
24V ASP 3.8 0.4 - - - -
340V TRP 2.9 1.0 + - - -
341V ILE* 3.3 0.4 - - - -
343V GLY* 1.3 70.2 - - - +
345V ILE* 1.3 56.3 + - - +
348V SER* 2.7 24.1 + - - -
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Residues in contact with ILE 345 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541G MET* 2.1 78.6 - - + +
637G LYS 0.8 53.2 - - - +
638G GLY* 0.5 210.9 - - - +
639G GLY* 1.9 17.5 - - - +
640G LYS* 6.0 1.8 - - + -
143V TYR* 3.5 4.3 - - + -
341V ILE* 3.7 0.4 - - + -
342V GLY 3.8 2.2 - - - +
344V SER* 1.3 65.7 - - - +
346V LEU* 1.3 54.3 - - - +
348V SER* 2.7 12.1 + - - -
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Residues in contact with LEU 346 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538G GLU* 4.2 5.2 - - - +
541G MET* 1.5 60.3 - - + +
542G PHE* 4.2 25.8 - - + -
104V LEU* 4.2 13.0 - - + -
133V TYR* 4.5 7.9 - - + +
135V ALA* 4.7 1.1 - - + -
140V LEU* 3.7 24.9 - - + -
143V TYR* 3.8 9.4 - - + -
342V GLY 3.1 14.6 + - - +
343V GLY 3.8 0.9 - - - +
345V ILE* 1.3 71.9 - - - +
347V ALA* 1.3 57.8 + - - +
349V LEU* 3.1 3.5 - - - +
352V PHE* 3.2 43.6 - - + +
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Residues in contact with ALA 347 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641G LYS* 4.7 1.2 + - - -
3V ASP 5.7 0.2 - - - +
7V ALA* 4.3 7.7 - - + +
9V VAL* 4.5 2.0 - - + -
22V ALA* 3.9 16.2 - - + -
104V LEU* 4.2 17.3 - - + -
343V GLY 2.8 22.5 + - - +
346V LEU* 1.3 75.1 - - - +
348V SER* 1.3 60.2 + - - +
349V LEU 3.6 3.8 + - - +
352V PHE* 3.9 13.0 - - - -
356V TRP* 4.1 30.0 + - + -
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Residues in contact with SER 348 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G MET* 4.4 0.3 - - - +
639G GLY* 3.0 8.0 - - - -
641G LYS* 1.8 38.5 + - - -
647G GLN* 1.1 142.4 + - - +
4V GLU 5.1 0.2 - - - -
7V ALA* 5.7 0.2 - - - -
22V ALA* 3.9 3.1 - - - +
23V GLY 4.0 2.0 - - - -
344V SER 2.7 24.4 + - - -
345V ILE 2.7 11.3 + - - -
347V ALA* 1.3 76.0 - - - +
349V LEU* 1.3 55.6 + - - +
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Residues in contact with LEU 349 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537G GLU 1.7 32.1 - - - +
538G GLU* 1.8 60.1 - - + +
540G CYS* 3.3 9.0 - - + +
541G MET* 1.6 100.4 - - + +
641G LYS* 4.0 3.0 + - - -
647G GLN* 4.3 9.4 - - + +
345V ILE 2.9 0.6 + - - -
346V LEU 3.1 2.2 + - - +
347V ALA 4.3 2.4 - - - +
348V SER* 1.3 72.2 + - - +
350V SER* 1.3 64.9 - - - +
351V THR 3.3 0.2 - - - -
352V PHE* 3.3 14.9 + - - +
353V GLN* 4.2 4.2 + - - +
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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