Contacts of the helix formed by residues 348 - 361 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340E TRP* 3.5 29.1 + + + +
341E ARG* 4.8 2.5 - - - +
342E ASP* 4.9 8.8 - - + +
346E GLY 4.7 5.2 - - - -
347E SER* 1.3 73.5 + - - +
349E TYR* 1.3 58.1 + - - +
351E GLU* 3.9 4.3 - - - +
352E THR* 2.7 37.9 + - - -
377E VAL* 4.3 9.6 - - + -
380E LYS* 3.6 58.2 - - + +
381E GLY* 3.9 11.4 - - - -
383E TYR 3.4 26.2 - - - -
385E GLN* 3.3 39.5 - - + +
186F LEU* 3.5 36.5 - - + +
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Residues in contact with TYR 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E PHE* 3.5 12.3 - - + -
283E GLN* 3.5 31.6 - - + +
330E SER* 2.6 38.2 + - - -
331E TYR 4.2 3.1 - - - -
332E SER* 3.4 38.4 - - - +
347E SER* 3.3 1.6 + - - +
348E TRP* 1.3 80.1 - - - +
350E VAL* 1.3 63.4 + - + +
352E THR* 3.3 2.3 + - - -
353E LEU* 2.7 62.3 + - + +
370E LEU* 4.3 1.7 - - + +
373E VAL* 4.0 24.0 - - + +
377E VAL* 4.2 8.5 - - + +
385E GLN* 4.2 8.2 + - - +
387E PRO* 4.2 10.5 - - + -
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Residues in contact with VAL 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ASP* 3.5 50.3 - - + +
188E LYS* 5.0 5.6 - - + +
189E LEU* 3.6 28.2 - - + +
235E LEU* 4.3 8.1 - - + -
283E GLN* 4.0 27.4 - - + -
347E SER* 3.6 3.4 + - - -
348E TRP 3.5 0.4 - - - -
349E TYR* 1.3 82.9 - - + +
351E GLU* 1.3 65.5 + - - +
353E LEU* 3.7 7.2 - - + +
354E ASP* 3.1 24.1 + - - +
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Residues in contact with GLU 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ASP* 4.4 3.2 + - - +
188E LYS* 3.8 27.6 + - - +
345E SER* 4.1 22.1 - - - +
346E GLY 4.5 3.7 - - - +
347E SER 3.0 20.0 + - - +
348E TRP* 3.9 5.3 - - - +
350E VAL* 1.3 76.7 - - - +
352E THR* 1.3 61.5 + - - +
354E ASP* 3.6 2.3 + - - +
355E ASP* 3.3 25.6 + - + +
380E LYS* 3.7 21.2 + - - -
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Residues in contact with THR 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348E TRP 2.7 23.5 + - - -
349E TYR 3.7 1.3 - - - -
351E GLU* 1.3 74.6 - - - +
353E LEU* 1.3 64.1 + - - +
355E ASP* 4.2 3.9 - - - +
356E ILE* 3.2 34.6 + - + +
373E VAL* 3.8 5.4 - - - +
376E ALA* 3.3 33.2 - - + -
377E VAL* 3.5 22.2 + - + +
380E LYS* 3.5 19.8 + - - -
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Residues in contact with LEU 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU* 4.3 20.4 - - + -
192E ARG* 5.6 1.6 - - + -
193E PHE* 5.5 4.3 - - + -
281E PHE* 4.1 17.9 - - + -
349E TYR* 2.7 56.7 + - + +
350E VAL* 3.7 8.3 - - + +
351E GLU 3.3 0.4 - - - -
352E THR* 1.3 73.1 - - - +
354E ASP* 1.3 60.4 + - - +
356E ILE* 3.4 1.6 + - - +
357E PHE* 2.9 70.3 + - + -
370E LEU* 4.2 7.2 - - + -
373E VAL* 3.8 13.4 - - + +
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Residues in contact with ASP 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LYS* 3.7 37.6 - - + +
189E LEU* 5.3 4.3 - - + -
192E ARG* 2.8 46.9 + - - +
350E VAL 3.1 17.7 + - - +
351E GLU 4.1 2.9 - - - +
353E LEU* 1.3 80.6 - - - +
355E ASP* 1.3 59.0 + - - +
357E PHE* 3.5 5.6 + - - +
358E GLU* 2.9 28.2 + - - +
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Residues in contact with ASP 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E GLU* 3.3 17.1 + - + +
352E THR* 4.2 5.4 - - - +
353E LEU 3.3 0.2 - - - -
354E ASP* 1.3 79.3 - - - +
356E ILE* 1.3 64.8 + - + +
358E GLU* 3.5 7.4 + - - +
359E GLN* 3.0 51.3 + - - +
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Residues in contact with ILE 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E THR* 3.2 28.5 + - + +
353E LEU 3.9 2.5 - - - +
355E ASP* 1.3 79.9 - - + +
357E PHE* 1.3 61.0 + - - +
359E GLN* 4.7 2.2 - - - +
360E TRP* 2.8 37.4 + - + +
369E LEU* 3.6 30.1 - - + +
372E ARG* 3.3 33.7 - - + +
373E VAL* 3.2 35.9 - - + +
376E ALA* 4.2 4.3 - - + -
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Residues in contact with PHE 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ARG* 3.9 25.5 + - + -
193E PHE* 4.7 9.0 - + - -
196E LEU* 4.2 21.1 - - + -
281E PHE* 4.7 7.2 - + - -
353E LEU* 2.9 53.4 + - + +
354E ASP 3.8 4.9 - - - +
356E ILE* 1.3 77.4 - - + +
358E GLU* 1.3 63.8 + - - +
361E ALA* 2.9 33.5 + - + +
366E LEU* 4.0 18.6 - - + -
369E LEU* 3.7 38.4 - - + -
370E LEU* 4.6 6.7 - - + -
373E VAL* 5.1 0.9 - - + -
400E PHE* 3.9 20.9 - + - -
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Residues in contact with GLU 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ARG* 2.7 42.4 + - - +
354E ASP 2.9 17.8 + - - +
355E ASP* 3.5 10.8 - - - +
356E ILE 3.3 0.2 - - - -
357E PHE* 1.3 79.8 - - - +
359E GLN* 1.3 67.0 + - + +
361E ALA* 4.7 0.9 + - - +
362E HIS* 4.8 5.4 + - - -
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Residues in contact with GLN 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E ASP* 3.0 38.4 + - - +
356E ILE* 5.2 1.3 - - - +
358E GLU* 1.3 83.8 - - + +
360E TRP* 1.3 95.4 + - + +
361E ALA 3.8 0.4 - - - -
362E HIS* 3.1 24.7 - - - -
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Residues in contact with TRP 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E ILE* 2.8 26.5 + - + +
359E GLN* 1.3 107.4 + - + +
361E ALA* 1.3 58.7 + - - +
362E HIS* 3.3 5.6 - + - -
363E SER* 3.8 18.4 - - - -
364E GLU* 3.1 47.6 + - + +
369E LEU* 3.6 10.9 - - + +
372E ARG* 3.3 54.9 - - - +
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Residues in contact with ALA 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ARG* 4.4 1.9 + - - -
192E ARG* 6.0 0.4 - - - +
196E LEU* 4.5 13.2 - - + -
357E PHE* 2.9 31.9 + - + +
358E GLU 4.7 0.4 + - - +
359E GLN 3.8 0.6 - - - -
360E TRP* 1.3 77.5 - - - +
362E HIS* 1.3 62.6 + - - +
364E GLU 3.5 11.6 - - - +
369E LEU* 3.8 18.0 - - + +
400E PHE* 4.1 15.4 + - + +
402E THR* 4.0 19.5 - - + +
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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