Contacts of the helix formed by residues 348 - 361 (chain I) in PDB entry 3V3K
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 TRP 348 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340I TRP* 3.6 27.4 + + + +
341I ARG* 4.9 2.3 - - - +
342I ASP* 5.0 8.2 - - + +
346I GLY 4.5 7.0 - - - -
347I SER* 1.3 73.7 + - - +
349I TYR* 1.3 60.5 + - - +
351I GLU* 4.1 4.8 - - - +
352I THR* 2.7 33.1 + - - -
377I VAL* 3.7 12.7 - - + +
380I LYS* 3.7 58.6 - - + +
381I GLY* 3.8 10.5 - - - -
383I TYR 3.4 27.4 - - - -
385I GLN* 3.3 39.3 - - + +
186J LEU* 3.4 38.6 - - + +
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Residues in contact with TYR 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I PHE* 3.6 12.2 - + + -
282I ILE 4.8 7.0 - - - -
283I GLN* 3.5 27.4 - - + +
330I SER* 2.6 36.4 + - - -
331I TYR 4.1 4.0 - - - -
332I SER* 3.5 38.6 - - - +
347I SER* 3.2 1.8 + - - +
348I TRP* 1.3 80.1 - - - +
350I VAL* 1.3 62.1 + - + +
352I THR* 3.7 1.9 - - - -
353I LEU* 2.8 61.7 + - + +
370I LEU* 4.3 2.8 - - + +
373I VAL* 3.9 21.6 - - + +
377I VAL* 4.3 8.0 - - + +
385I GLN* 4.4 7.0 + - - +
387I PRO* 4.2 10.8 - - + -
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Residues in contact with VAL 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I ASP* 3.5 55.0 - - + +
188I LYS* 4.8 6.5 - - + -
189I LEU* 3.7 22.4 - - + -
235I LEU* 4.3 8.3 - - + -
283I GLN* 4.1 19.3 - - + -
347I SER* 3.5 11.9 + - - -
348I TRP 3.5 0.2 - - - -
349I TYR* 1.3 80.7 - - + +
351I GLU* 1.3 61.7 + - - +
353I LEU* 4.1 5.6 - - + -
354I ASP* 2.9 31.2 + - - +
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Residues in contact with GLU 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I ASP* 4.3 1.9 + - - +
188I LYS* 3.8 27.8 + - - +
342I ASP* 5.7 0.2 - - - +
345I SER* 3.7 30.8 - - - +
346I GLY 4.3 3.3 - - - +
347I SER 3.0 20.2 + - - +
348I TRP* 4.1 6.6 - - - +
350I VAL* 1.3 77.2 - - - +
352I THR* 1.3 60.9 + - - +
354I ASP* 4.1 1.7 - - - +
355I ASP* 3.3 24.6 + - + +
380I LYS* 3.9 21.0 + - - +
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Residues in contact with THR 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I TRP 2.7 23.8 + - - -
349I TYR 3.8 2.2 - - - -
351I GLU* 1.3 73.7 - - - +
353I LEU* 1.3 60.1 + - - +
355I ASP* 3.5 4.5 + - + +
356I ILE* 3.0 42.9 + - + +
373I VAL* 3.8 13.2 - - - +
376I ALA* 3.3 31.8 - - + +
377I VAL* 3.6 11.6 - - - +
380I LYS* 3.7 18.9 + - - -
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Residues in contact with LEU 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LEU* 4.3 21.8 - - + -
192I ARG* 5.6 1.1 - - + -
193I PHE* 5.6 1.6 - - + -
281I PHE* 3.5 23.1 - - + -
349I TYR* 2.8 59.3 + - + +
350I VAL* 3.2 7.4 + - + +
352I THR* 1.3 74.0 - - - +
354I ASP* 1.3 58.4 + - - +
356I ILE* 4.0 0.3 - - - +
357I PHE* 2.9 71.9 + - + -
370I LEU* 4.4 3.8 - - + -
373I VAL* 3.9 15.2 - - + +
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Residues in contact with ASP 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I LYS* 3.5 53.3 - - + +
189I LEU* 5.3 3.1 - - + -
192I ARG* 2.9 36.4 + - - +
350I VAL* 2.9 18.4 + - + +
351I GLU 4.1 3.1 - - - +
353I LEU* 1.3 81.6 - - - +
355I ASP* 1.3 56.2 + - - +
357I PHE* 3.9 4.4 - - - +
358I GLU* 3.1 26.7 + - - +
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Residues in contact with ASP 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I GLU* 3.3 17.2 + - + +
352I THR* 3.8 7.0 - - - +
353I LEU 3.3 0.2 - - - -
354I ASP* 1.3 79.4 - - - +
356I ILE* 1.3 66.5 + - + +
358I GLU* 3.4 7.8 + - - +
359I GLN* 2.9 50.1 + - - +
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Residues in contact with ILE 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352I THR* 3.0 29.3 + - + +
355I ASP* 1.3 79.1 - - + +
357I PHE* 1.3 60.8 + - + +
359I GLN* 4.8 2.0 - - - +
360I TRP* 3.0 37.7 + - + +
369I LEU* 3.7 29.6 - - + +
372I ARG* 3.3 34.1 - - + +
373I VAL* 3.2 40.4 - - + +
376I ALA* 4.3 3.6 - - + -
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Residues in contact with PHE 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I ARG* 3.8 27.7 + - + -
193I PHE* 4.8 8.3 - + - -
196I LEU* 4.0 23.1 - - + -
281I PHE* 4.4 7.6 - + - -
353I LEU* 2.9 54.9 + - + +
354I ASP 3.9 2.2 - - - +
356I ILE* 1.3 77.5 - - + +
358I GLU* 1.3 63.6 + - - +
361I ALA* 2.9 33.8 + - + +
366I LEU* 4.2 17.9 - - + -
369I LEU* 3.7 37.2 - - + -
370I LEU* 4.6 6.7 - - + -
373I VAL* 5.2 0.9 - - + -
400I PHE* 4.1 20.9 - + - -
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Residues in contact with GLU 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I ARG* 2.9 39.6 + - - +
354I ASP 3.1 10.2 + - - +
355I ASP* 3.5 12.3 - - - +
356I ILE 3.3 0.4 - - - -
357I PHE* 1.3 78.3 - - - +
359I GLN* 1.3 65.9 + - + +
361I ALA* 5.5 0.2 - - - +
362I HIS* 4.8 6.8 + - - -
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Residues in contact with GLN 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I ASP* 2.9 39.8 + - - +
356I ILE* 3.4 1.6 + - - +
358I GLU* 1.3 83.1 - - + +
360I TRP* 1.3 96.4 + - + +
361I ALA 3.9 0.4 - - - -
362I HIS* 3.2 22.2 - - - -
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Residues in contact with TRP 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I ILE* 3.0 21.1 + - + +
359I GLN* 1.3 110.4 + - + +
361I ALA* 1.3 60.0 + - - +
362I HIS* 3.3 4.3 - - - -
363I SER* 3.3 18.7 + - - -
364I GLU* 3.0 56.3 + - - +
369I LEU* 3.7 13.9 - - + +
372I ARG* 3.5 45.7 - - - +
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Residues in contact with ALA 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ARG* 4.1 6.1 + - - -
192I ARG* 6.2 0.2 - - - -
196I LEU* 4.6 9.6 - - + -
357I PHE* 2.9 33.4 + - + +
358I GLU 4.8 0.2 + - - -
359I GLN 3.9 0.6 - - - -
360I TRP* 1.3 77.9 - - - +
362I HIS* 1.3 62.0 + - - +
363I SER 3.5 0.2 + - - -
364I GLU 3.5 11.5 - - - +
369I LEU* 3.9 18.3 - - + +
400I PHE* 4.3 16.2 + - + +
402I THR* 4.1 18.6 - - + -
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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