Contacts of the helix formed by residues 337 - 349 (chain 7) 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 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187 LYS* 3.8 21.1 - - + -
267 ALA* 4.5 11.9 - - + -
277 PRO* 3.6 41.5 - - + -
307 VAL* 4.1 18.6 - - + +
3347 GLU* 2.8 15.1 + - + +
3367 LYS* 1.3 123.0 + - + +
3387 SER* 1.4 62.4 + - - -
3397 VAL* 3.3 3.4 - - - -
3407 TRP* 3.0 8.8 + - + +
3417 ILE* 2.9 39.3 + - + +
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Residues in contact with SER 338 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1407 LEU 3.8 0.3 - - - +
1417 SER* 3.2 27.1 + - - -
1447 ALA* 3.5 11.6 - - - +
2987 VAL* 5.9 1.5 - - - +
2997 MET 4.4 2.6 + - - -
3007 SER* 3.7 16.2 - - - -
3327 PRO* 5.2 6.1 - - - +
3347 GLU* 3.8 9.1 + - - -
3357 ARG* 3.3 24.4 + - - +
3377 TYR* 1.4 72.6 - - - +
3397 VAL* 1.3 54.7 - - - +
3417 ILE* 3.1 7.6 + - - +
3427 GLY* 2.8 31.9 + - - -
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Residues in contact with VAL 339 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117 ASP* 3.4 33.9 - - - +
1067 THR* 4.2 2.7 - - + -
1377 GLN* 4.0 25.8 - - + +
1407 LEU* 3.3 26.0 - - + +
1417 SER* 3.1 24.0 + - - +
1547 ASP* 4.2 16.6 - - - +
3007 SER* 4.5 4.7 - - - +
3357 ARG 6.1 0.2 - - - +
3377 TYR* 5.0 1.3 - - - -
3387 SER* 1.3 81.4 - - - +
3407 TRP* 1.3 60.9 + - - +
3437 GLY 3.2 14.6 + - - -
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Residues in contact with TRP 340 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97 VAL* 2.8 42.7 + - + +
117 ASP* 4.0 9.6 - - + +
187 LYS* 3.4 39.3 + - + -
197 ALA* 3.6 5.9 - - - +
207 GLY* 3.6 27.1 - - - -
217 PHE 3.5 22.7 - - - -
247 ASP* 3.8 17.9 - - + -
257 ASP 4.3 0.7 - - - -
267 ALA* 3.5 28.0 - - - -
277 PRO* 3.7 16.2 - - + -
1067 THR* 6.2 0.7 - - - -
3377 TYR* 3.0 18.3 + - + +
3397 VAL* 1.3 77.7 - - - +
3417 ILE* 1.3 67.9 + - + +
3437 GLY* 3.0 4.2 + - - -
3447 SER* 2.9 33.3 + - - -
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Residues in contact with ILE 341 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 ASP* 3.5 27.6 - - - +
267 ALA* 5.6 0.2 - - + -
1447 ALA* 4.5 6.3 - - + +
3347 GLU* 3.7 42.0 - - + +
3377 TYR* 2.9 35.5 + - + +
3387 SER* 3.6 5.2 - - - +
3407 TRP* 1.3 85.0 - - + +
3427 GLY* 1.3 57.6 + - - +
3447 SER* 3.0 7.3 + - - -
3457 ILE* 3.0 46.2 + - + +
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Residues in contact with GLY 342 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1407 LEU* 3.4 31.6 - - - +
1437 TYR* 3.7 7.5 - - - -
1447 ALA* 3.5 15.3 - - - +
3387 SER 2.8 11.1 + - - -
3397 VAL 3.8 1.1 - - - -
3417 ILE* 1.3 75.9 - - - +
3437 GLY* 1.3 54.7 + - - +
3457 ILE* 3.8 3.1 - - - +
3467 LEU* 3.1 30.5 + - - +
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Residues in contact with GLY 343 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97 VAL* 3.8 16.1 - - - +
1047 LEU* 4.3 7.3 - - - +
1407 LEU* 3.8 18.8 - - - +
3397 VAL 3.2 8.8 + - - -
3407 TRP 3.0 6.7 + - - -
3427 GLY* 1.3 75.0 - - - +
3447 SER* 1.3 53.9 + - - +
3467 LEU* 3.8 1.7 - - - +
3477 ALA* 2.8 38.3 + - - +
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Residues in contact with SER 344 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97 VAL* 3.9 10.4 - - - +
217 PHE 3.7 1.9 + - - -
227 ALA* 3.4 4.9 - - - +
237 GLY 2.8 28.2 + - - -
247 ASP 3.0 15.4 + - - -
3407 TRP* 2.9 30.0 + - - -
3417 ILE* 3.3 11.4 - - - -
3437 GLY* 1.3 71.7 - - - +
3457 ILE* 1.3 58.0 + - - +
3487 SER* 2.7 35.9 + - - -
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Residues in contact with ILE 345 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 TYR* 3.5 28.5 - - + +
1447 ALA* 4.4 19.1 - - - +
3417 ILE* 3.0 39.0 + - + +
3427 GLY 3.8 3.8 - - - +
3447 SER* 1.3 74.0 - - - +
3467 LEU* 1.3 66.3 + - - +
3487 SER* 2.7 21.4 + - - -
3497 LEU* 2.9 21.3 + - + +
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Residues in contact with LEU 346 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047 LEU* 4.2 12.1 - - + -
1337 TYR* 4.5 8.3 - - + +
1357 ALA* 4.7 1.3 - - + -
1407 LEU* 3.7 24.7 - - + -
1437 TYR* 3.8 23.6 - - + +
3427 GLY 3.1 14.4 + - - +
3437 GLY 3.8 1.3 - - - +
3457 ILE* 1.3 80.2 - - - +
3477 ALA* 1.3 61.7 + - - +
3497 LEU* 3.1 23.7 - - + +
3527 PHE* 3.2 48.2 - - + +
3557 MET* 5.5 3.8 - - + -
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Residues in contact with ALA 347 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ASP 5.7 0.5 - - - +
77 ALA* 4.3 8.1 - - + +
97 VAL* 4.5 2.2 - - + -
227 ALA* 3.9 15.9 - - + -
1047 LEU* 4.2 17.3 - - + -
3437 GLY 2.8 22.7 + - - +
3467 LEU* 1.3 75.0 - - - +
3487 SER* 1.3 60.4 + - - +
3497 LEU 3.3 3.9 + - - +
3527 PHE* 3.9 12.5 - - - -
3567 TRP* 4.1 29.6 + - + -
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Residues in contact with SER 348 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 GLU* 5.0 18.9 - - - +
77 ALA* 5.7 0.2 - - - -
227 ALA* 3.9 6.9 - - - +
237 GLY* 4.0 20.2 + - - -
3447 SER 2.7 24.4 + - - -
3457 ILE* 2.7 14.6 + - - -
3477 ALA* 1.3 76.7 - - - +
3497 LEU* 1.3 66.2 + - - +
3507 SER* 3.6 1.4 + - - -
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Residues in contact with LEU 349 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 TYR* 4.2 18.8 - - - +
3457 ILE* 2.9 24.4 + - + +
3467 LEU* 3.1 20.1 + - + +
3477 ALA 4.3 2.4 - - - +
3487 SER* 1.3 80.3 - - - +
3507 SER* 1.3 79.9 - - - +
3517 THR* 3.2 29.2 - - - +
3527 PHE* 3.3 18.5 + - + +
3537 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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