Contacts of the helix formed by residues 337 - 349 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189 LYS* 3.8 20.9 - - + -
269 ALA* 4.5 11.0 - - + -
279 PRO* 3.6 41.3 - - + -
309 VAL* 4.1 18.9 - - + +
3349 GLU* 2.8 12.6 + - + +
3369 LYS* 1.3 125.3 + - + +
3389 SER* 1.4 61.9 + - - -
3399 VAL* 3.3 3.6 - - - -
3409 TRP* 3.0 8.4 + - + -
3419 ILE* 2.9 38.8 + - + +
410D ASN* 4.9 5.8 - - + -
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Residues in contact with SER 338 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409 LEU 3.8 0.2 - - - +
1419 SER* 3.2 28.0 + - - -
1449 ALA* 3.5 11.7 - - - +
2989 VAL* 5.9 0.2 - - - +
2999 MET 4.4 2.6 + - - -
3009 SER* 3.7 16.0 - - - -
3329 PRO* 5.2 5.7 - - - +
3349 GLU* 3.8 7.3 + - - -
3359 ARG* 3.3 24.3 + - - +
3369 LYS 3.8 0.2 - - - -
3379 TYR* 1.4 72.3 - - - +
3399 VAL* 1.3 55.5 - - - +
3419 ILE* 3.1 8.2 + - - +
3429 GLY* 2.8 31.2 + - - -
636D LYS 5.2 0.9 - - - -
637D LYS* 4.9 5.9 + - - +
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Residues in contact with VAL 339 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119 ASP* 3.4 34.3 - - - +
1069 THR* 4.2 2.5 - - + -
1379 GLN* 4.0 25.6 - - + +
1409 LEU* 3.3 26.4 - - + +
1419 SER* 3.1 24.7 - - - +
1549 ASP* 4.2 17.7 - - - +
3009 SER* 4.5 3.6 - - - +
3359 ARG 6.1 0.2 - - - +
3379 TYR 5.0 1.1 - - - -
3389 SER* 1.3 81.5 - - - +
3409 TRP* 1.3 60.4 + - - +
3439 GLY* 3.2 14.4 + - - -
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Residues in contact with TRP 340 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99 VAL* 2.8 42.7 + - + +
119 ASP* 4.0 9.9 - - + +
189 LYS* 3.4 38.0 + - + -
199 ALA* 3.6 6.6 - - - +
209 GLY* 3.6 27.1 - - - -
219 PHE 3.5 10.5 - - - -
249 ASP* 3.8 3.4 - - + -
259 ASP 4.3 0.7 - - - -
269 ALA* 3.5 28.0 - - - -
279 PRO* 3.7 16.2 - - + -
3379 TYR* 3.0 18.1 + - + +
3399 VAL* 1.3 78.6 - - - +
3419 ILE* 1.3 61.1 + - + +
3439 GLY* 3.0 4.0 + - - -
3449 SER 2.9 11.4 + - - -
642D LYS* 2.5 71.4 + - + -
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Residues in contact with ILE 341 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259 ASP 3.5 15.5 - - - +
3349 GLU* 3.7 16.4 - - + +
3379 TYR* 2.9 35.9 + - + +
3389 SER* 3.6 4.9 - - - +
3409 TRP* 1.3 79.5 - - + +
3429 GLY* 1.3 51.1 - - - +
3449 SER* 5.3 0.2 - - - -
3459 ILE 3.0 2.1 + - - -
633D GLY* 5.5 2.7 - - - -
635D GLY* 2.7 64.8 - - - +
636D LYS 3.2 13.9 - - - +
637D LYS 3.4 9.2 - - - -
638D GLY* 2.0 35.7 - - - -
639D GLY 4.9 0.7 - - - +
642D LYS* 2.9 16.7 + - - +
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Residues in contact with GLY 342 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409 LEU* 3.4 31.1 - - - +
1439 TYR* 3.7 7.9 - - - -
1449 ALA* 3.5 13.1 - - - +
3389 SER 2.8 10.9 + - - -
3399 VAL 3.8 0.9 - - - -
3409 TRP 3.2 0.2 - - - -
3419 ILE* 1.3 76.6 - - - +
3439 GLY* 1.3 55.0 + - - +
3459 ILE* 3.8 0.2 - - - +
3469 LEU* 3.1 29.8 + - - +
637D LYS 4.0 0.2 - - - -
638D GLY* 3.7 4.0 - - - -
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Residues in contact with GLY 343 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99 VAL* 3.8 15.3 - - - -
1049 LEU* 4.3 6.8 - - - +
1409 LEU* 3.8 19.0 - - - +
3399 VAL 3.2 8.2 + - - -
3409 TRP 3.0 7.8 + - - -
3429 GLY* 1.3 75.2 - - - +
3449 SER* 1.3 54.7 + - - +
3469 LEU* 3.8 2.1 - - - +
3479 ALA* 2.8 39.2 + - - +
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Residues in contact with SER 344 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99 VAL* 3.9 6.0 - - - +
229 ALA* 3.7 1.4 - - - +
239 GLY 2.8 1.4 + - - -
249 ASP 3.8 0.4 - - - -
3409 TRP 2.9 1.4 + - - -
3419 ILE* 3.3 0.7 - - - -
3439 GLY* 1.3 69.1 - - - +
3459 ILE* 1.3 56.7 + - - +
3489 SER* 2.7 24.1 + - - -
639D GLY* 2.4 25.8 + - - -
642D LYS* 0.7 190.6 - - - +
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Residues in contact with ILE 345 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439 TYR* 3.5 4.0 - - + -
3419 ILE* 3.0 0.4 + - + -
3429 GLY 3.8 2.2 - - - +
3449 SER* 1.3 65.1 - - - +
3469 LEU* 1.3 55.1 - - - +
3489 SER* 2.7 12.3 + - - -
541D MET* 2.1 77.7 - - + +
637D LYS 0.8 52.3 - - - +
638D GLY* 0.5 204.3 - - - +
639D GLY* 1.9 17.2 - - - +
640D LYS* 4.7 2.2 - - + +
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Residues in contact with LEU 346 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049 LEU* 4.2 12.3 - - + -
1339 TYR* 4.5 7.6 - - + -
1359 ALA* 4.7 0.9 - - + -
1409 LEU* 3.7 25.1 - - + -
1439 TYR* 3.8 9.4 - - + -
3429 GLY 3.1 14.3 + - - +
3439 GLY 3.8 1.1 - - - +
3459 ILE* 1.3 71.5 - - - +
3479 ALA* 1.3 58.8 + - - +
3499 LEU* 3.1 3.6 + - - +
3529 PHE* 3.2 43.4 - - + +
538D GLU* 4.2 5.6 - - + +
541D MET* 1.5 82.9 - - + +
542D PHE* 4.2 25.8 - - + -
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Residues in contact with ALA 347 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39 ASP 5.7 0.2 - - - +
79 ALA* 4.3 8.0 - - + +
99 VAL* 4.5 2.0 - - + -
229 ALA* 3.9 16.8 - - + -
1049 LEU* 4.2 17.7 - - + -
3439 GLY 2.8 22.3 + - - +
3469 LEU* 1.3 74.8 - - - +
3489 SER* 1.3 60.5 + - - +
3499 LEU 4.3 3.6 - - - +
3529 PHE* 3.9 11.9 - - - -
3569 TRP* 4.1 28.9 + - + -
641D LYS* 4.7 1.2 + - - -
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Residues in contact with SER 348 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49 GLU 5.1 0.2 - - - -
229 ALA* 3.9 3.5 - - - +
239 GLY 4.0 2.2 - - - -
3449 SER 2.7 24.0 + - - -
3459 ILE 2.7 10.9 + - - -
3479 ALA* 1.3 75.6 - - - +
3499 LEU* 1.3 55.9 + - - +
541D MET* 4.4 0.7 - - - +
639D GLY* 3.0 7.8 - - - -
641D LYS* 1.8 38.2 + - - +
647D GLN* 1.1 140.8 - - - +
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Residues in contact with LEU 349 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3469 LEU 3.1 1.8 + - - +
3479 ALA 4.3 1.9 - - - +
3489 SER* 1.3 72.6 - - - +
3509 SER* 1.3 64.8 - - - +
3529 PHE* 3.3 15.2 + - - +
3539 GLN* 4.2 4.3 + - - +
537D GLU 1.7 33.4 - - - +
538D GLU* 1.8 60.3 - - + +
540D CYS* 3.3 9.0 - - + +
541D MET* 1.6 100.4 - - + +
641D LYS* 4.0 2.9 + - - -
647D GLN* 4.3 9.9 - - + +
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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