Contacts of the helix formed by residues 337 - 349 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182 LYS* 3.8 20.9 - - + -
262 ALA* 4.5 11.4 - - + -
272 PRO* 3.6 42.0 - - + -
302 VAL* 4.1 18.6 - - + +
3342 GLU* 2.8 10.1 + - + +
3362 LYS* 1.3 128.5 + - + +
3382 SER* 1.4 62.3 + - - -
3392 VAL* 3.3 3.6 - - - -
3402 TRP* 3.0 8.4 + - + -
3412 ILE* 2.9 39.3 + - + +
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Residues in contact with SER 338 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402 LEU 3.8 0.3 - - - +
1412 SER* 3.2 27.9 + - - -
1442 ALA* 3.5 11.5 - - - +
2982 VAL* 5.9 1.3 - - - +
2992 MET 4.4 2.4 + - - -
3002 SER* 3.7 15.5 - - - -
3322 PRO* 5.2 5.9 - - - +
3342 GLU* 3.8 8.5 + - - -
3352 ARG* 3.3 24.6 + - - +
3362 LYS 3.8 0.2 - - - -
3372 TYR* 1.4 72.8 - - - +
3392 VAL* 1.3 54.5 - - - +
3412 ILE* 3.1 8.1 + - - +
3422 GLY* 2.8 32.2 + - - -
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Residues in contact with VAL 339 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112 ASP* 3.4 34.1 - - - +
1062 THR* 4.2 2.5 - - + -
1372 GLN* 4.0 26.0 - - + +
1402 LEU* 3.3 26.4 - - + +
1412 SER* 3.1 23.8 + - - +
1542 ASP* 4.2 17.3 - - - +
3002 SER* 4.5 4.3 - - - +
3352 ARG 6.1 0.4 - - - +
3372 TYR* 5.0 1.3 - - - -
3382 SER* 1.3 81.4 - - - +
3402 TRP* 1.3 61.3 + - - +
3432 GLY 3.2 14.2 + - - -
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Residues in contact with TRP 340 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 VAL* 2.8 44.7 + - + +
112 ASP* 4.0 10.5 - - + +
182 LYS* 3.4 37.9 + - + -
192 ALA* 3.6 6.6 - - - +
202 GLY* 3.6 27.4 - - - -
212 PHE 3.5 23.1 - - - -
242 ASP* 3.8 18.2 - - + -
252 ASP 4.3 0.7 - - - -
262 ALA* 3.5 28.7 - - - -
272 PRO* 3.7 16.8 - - + -
1402 LEU* 5.7 0.2 - - - -
3372 TYR* 3.0 18.1 + - + +
3392 VAL* 1.3 79.2 - - - +
3412 ILE* 1.3 66.8 + - + +
3432 GLY* 3.0 4.2 + - - -
3442 SER* 2.9 33.4 + - - -
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Residues in contact with ILE 341 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 ASP* 3.5 27.1 - - - +
262 ALA* 5.6 0.2 - - + -
1442 ALA* 4.5 7.2 - - + +
3342 GLU* 3.7 41.3 - - + +
3372 TYR* 2.9 37.0 + - + +
3382 SER* 3.6 5.2 - - - +
3402 TRP* 1.3 84.6 - - + +
3422 GLY* 1.3 57.6 + - - +
3442 SER* 3.0 7.1 + - - -
3452 ILE* 3.0 46.3 + - + +
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Residues in contact with GLY 342 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402 LEU* 3.4 30.7 - - - +
1432 TYR* 3.7 8.1 - - - -
1442 ALA* 3.5 15.1 - - - +
3382 SER 2.8 11.1 + - - -
3392 VAL 3.8 0.9 - - - -
3412 ILE* 1.3 75.7 - - - +
3432 GLY* 1.3 55.6 + - - +
3452 ILE* 3.7 2.8 + - - +
3462 LEU* 3.1 29.8 + - - +
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Residues in contact with GLY 343 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 VAL* 3.9 15.9 - - - -
1042 LEU* 4.3 6.8 - - - +
1402 LEU* 3.8 19.0 - - - +
3392 VAL 3.2 7.7 + - - -
3402 TRP 3.0 7.8 + - - -
3422 GLY* 1.3 75.9 - - - +
3442 SER* 1.3 54.9 + - - +
3462 LEU* 3.8 1.9 - - - +
3472 ALA* 2.8 38.5 + - - +
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Residues in contact with SER 344 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 VAL* 3.9 11.1 - - - +
212 PHE 3.7 1.6 + - - -
222 ALA* 3.4 5.8 - - - +
232 GLY 2.8 28.1 + - - -
242 ASP 3.0 16.1 + - - -
3402 TRP* 2.9 29.4 + - - -
3412 ILE* 3.3 11.0 - - - -
3432 GLY* 1.3 71.8 - - - +
3452 ILE* 1.3 57.5 + - - +
3482 SER* 2.7 35.7 + - - -
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Residues in contact with ILE 345 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1432 TYR* 3.5 28.7 - - + +
1442 ALA* 4.4 18.8 - - - +
3412 ILE* 3.0 40.0 + - + +
3422 GLY* 3.8 3.8 - - - +
3442 SER* 1.3 73.5 - - - +
3462 LEU* 1.3 66.2 + - - +
3482 SER* 2.7 21.5 + - - -
3492 LEU* 2.9 21.2 + - + +
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Residues in contact with LEU 346 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042 LEU* 4.2 12.1 - - + -
1332 TYR* 4.5 7.6 - - + -
1352 ALA* 4.7 1.6 - - + -
1402 LEU* 3.7 24.9 - - + -
1432 TYR* 3.8 25.1 - - + +
3422 GLY 3.1 14.2 + - - +
3432 GLY 3.8 1.3 - - - +
3452 ILE* 1.3 81.2 - - - +
3472 ALA* 1.3 61.6 + - - +
3492 LEU* 3.1 23.8 - - + +
3522 PHE* 3.2 47.7 - - + +
3552 MET* 5.5 3.4 - - + -
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Residues in contact with ALA 347 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 ASP 5.7 0.3 - - - +
72 ALA* 4.3 7.0 - - + +
92 VAL* 4.5 2.0 - - + -
222 ALA* 3.9 16.4 - - + -
1042 LEU* 4.2 17.3 - - + -
3432 GLY 2.8 21.7 + - - +
3462 LEU* 1.3 75.2 - - - +
3482 SER* 1.3 61.4 + - - +
3492 LEU 4.3 3.6 - - - +
3522 PHE* 3.9 12.8 - - - -
3562 TRP* 4.1 29.9 + - + -
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Residues in contact with SER 348 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 GLU* 5.0 19.6 - - - +
72 ALA* 5.7 0.2 - - - -
222 ALA* 3.9 6.9 - - - +
232 GLY* 4.0 20.5 + - - -
3442 SER 2.7 24.1 + - - -
3452 ILE* 2.7 14.4 + - - -
3472 ALA* 1.3 76.0 - - - +
3492 LEU* 1.3 66.1 + - - +
3502 SER* 3.6 1.6 + - - -
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Residues in contact with LEU 349 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1432 TYR* 4.2 18.8 - - - +
3452 ILE* 2.9 23.8 + - + +
3462 LEU* 3.1 20.1 + - + +
3472 ALA 4.3 2.1 - - - +
3482 SER* 1.3 81.0 + - - +
3502 SER* 1.3 80.9 - - - +
3512 THR* 3.2 29.2 - - - +
3522 PHE* 3.3 18.8 + - + +
3532 GLN* 4.2 3.6 + - - +
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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