Contacts of the helix formed by residues 385 - 395 (chain H) in PDB entry 3WTV
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 ASN 385 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369H ASP* 5.6 4.5 - - - +
372H ALA* 3.5 18.2 - - + -
373H ARG* 5.0 3.4 - - - +
383H LYS* 3.7 20.4 + - - +
384H MET* 1.3 90.1 + - - +
386H TYR* 1.3 59.3 + - - +
387H GLU* 2.9 37.6 - - + +
388H LYS* 3.2 20.5 + - - +
389H LEU 2.9 23.6 + - - -
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Residues in contact with TYR 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365H LEU* 3.6 29.4 - - + -
368H PRO* 4.3 21.3 - - + +
369H ASP* 5.1 1.5 - - - +
371H VAL* 5.0 5.8 - - + -
372H ALA* 3.4 7.8 - - + +
385H ASN* 1.3 72.8 - - - +
387H GLU* 1.3 59.6 + - + +
389H LEU* 4.0 13.5 - - + -
390H SER* 2.7 52.7 + - - -
393H LEU* 5.1 5.6 - - + -
404H LYS* 4.8 1.2 - - - -
410H TYR* 3.9 38.1 + + - -
412H TYR* 2.6 38.5 + + - -
2J G 5.6 5.5 + - - -
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Residues in contact with GLU 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H ASN* 2.9 22.4 - - + +
386H TYR* 1.3 81.5 - - + +
388H LYS* 1.3 59.1 + - + +
390H SER* 2.7 17.9 + - - -
391H ARG* 4.2 3.1 + - - +
394H ARG* 4.3 6.4 + - - -
12I C 5.9 1.0 + - - -
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Residues in contact with LYS 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H LYS* 3.1 30.9 + - - +
384H MET* 4.0 11.2 - - - -
385H ASN* 3.2 21.3 + - - +
387H GLU* 1.3 78.2 - - + +
389H LEU* 1.3 66.5 + - - +
390H SER 3.1 2.2 - - - -
391H ARG* 3.0 20.0 + - - +
392H GLY 3.4 3.3 + - - -
9I A 4.4 12.5 + - + -
10I T 2.9 71.6 + - + +
11I C 3.7 27.9 + - + -
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Residues in contact with LEU 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H LEU* 3.4 34.9 - - + +
341H LEU* 4.7 7.4 - - + -
371H VAL* 3.6 47.6 - - + +
372H ALA* 4.0 6.5 - - + -
375H TRP* 4.3 7.0 - - + -
384H MET* 3.5 15.4 - - + +
385H ASN 2.9 16.3 + - - +
386H TYR* 3.9 12.3 - - + +
388H LYS* 1.3 76.5 - - - +
390H SER* 1.3 64.4 + - - +
392H GLY* 3.0 13.6 + - - -
393H LEU* 3.2 21.9 + - + -
9I A 5.2 5.4 - - - -
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Residues in contact with SER 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H TYR* 2.7 36.1 + - - -
387H GLU* 2.7 28.8 + - - -
389H LEU* 1.3 78.3 - - - +
391H ARG* 1.3 54.6 + - - -
393H LEU* 2.7 35.4 + - - +
394H ARG* 2.9 36.4 + - - +
412H TYR* 4.7 4.0 - - - -
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Residues in contact with ARG 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387H GLU 4.7 0.7 - - - +
388H LYS* 3.0 14.4 + - - +
390H SER* 1.3 79.7 + - - +
392H GLY* 1.3 63.9 + - - +
394H ARG* 3.1 24.1 + - - +
395H TYR* 3.0 65.4 + - + +
9I A 5.5 0.2 - - - +
10I T 3.7 26.2 - - + +
11I C 4.1 3.6 - - - +
4J G 3.1 49.9 + - - +
5J G 2.7 45.8 + - - -
6J A 5.6 0.2 + - - -
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Residues in contact with GLY 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337H LEU* 4.1 6.1 - - - -
388H LYS 3.4 3.8 + - - -
389H LEU* 3.0 11.2 + - - -
391H ARG* 1.3 79.7 - - - +
393H LEU* 1.3 61.9 + - - +
395H TYR* 3.2 24.3 + - - +
396H TYR* 3.2 21.3 - - - -
8I C 4.5 20.0 - - - +
9I A 5.7 1.6 - - - -
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Residues in contact with LEU 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H LEU* 3.8 23.1 - - + +
341H LEU* 4.0 15.0 - - + -
363H PHE* 5.6 1.6 - - + -
386H TYR* 5.1 4.0 - - + +
389H LEU* 3.2 17.5 + - + +
390H SER* 2.7 18.4 + - - +
392H GLY* 1.3 72.9 - - - +
394H ARG* 1.3 57.0 + - + +
396H TYR* 2.9 30.7 + - + +
397H TYR* 3.8 9.2 + - - -
402H ILE* 3.7 36.0 - - + +
412H TYR* 3.6 48.2 - - + +
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Residues in contact with ARG 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H GLU 4.3 4.9 + - - -
390H SER* 2.9 38.2 + - - +
391H ARG* 3.1 38.1 + - - +
393H LEU* 1.3 70.3 - - - +
395H TYR* 1.3 62.8 + - - +
396H TYR 2.9 6.0 + - - -
397H TYR* 3.2 51.3 + - + +
398H ASP* 3.8 4.0 - - - +
412H TYR* 5.6 2.2 + - + -
11I C 5.7 0.2 - - - +
12I C 5.1 1.4 - - - +
2J G 4.5 7.0 - - - +
3J A 3.4 45.3 + - + +
4J G 2.8 44.5 + - + -
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Residues in contact with TYR 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391H ARG* 3.0 62.0 + - + +
392H GLY* 3.4 13.7 - - - +
393H LEU 3.2 0.6 - - - -
394H ARG* 1.3 75.8 - - - +
396H TYR* 1.3 61.3 + - + +
397H TYR 3.5 0.2 - - - -
398H ASP* 3.1 26.3 - - - +
399H LYS* 3.7 27.1 - - - +
8I C 4.3 32.3 - + + +
9I A 2.8 33.9 + - - -
6J A 3.0 16.1 + - - -
7J T 3.8 4.9 + - - -
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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