Contacts of the helix formed by residues 308 - 322 (chain B) in PDB entry 1V40
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 LYS 308 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306B GLU* 2.8 35.5 + - - +
307B LYS* 1.3 77.3 - - + +
309B GLN* 1.3 49.2 + - - +
310B ASP* 2.6 29.4 + - - +
311B VAL* 3.2 26.2 - - + +
312B LYS* 2.8 26.3 + - - +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU 3.3 19.8 + - - -
307B LYS* 3.0 24.6 + - - +
308B LYS* 1.3 67.4 - - - +
310B ASP* 1.3 56.5 + - - +
312B LYS* 3.5 31.0 + - - +
313B GLU* 3.3 24.1 + - - +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LYS* 2.6 25.9 + - - +
309B GLN* 1.3 71.7 - - - +
311B VAL* 1.3 77.2 + - - +
312B LYS 2.9 4.7 - - - -
313B GLU* 2.9 21.1 + - - +
314B GLN* 3.0 17.0 + - - +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU* 3.8 12.5 - - + +
308B LYS* 3.2 46.7 - - + +
310B ASP* 1.3 90.5 + - - +
312B LYS* 1.3 63.0 + - - +
314B GLN* 3.5 10.8 + - + -
315B MET* 2.9 44.5 - - + +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PRO* 3.4 31.2 - - + +
304B TRP* 3.4 19.0 + - - +
306B GLU* 3.6 29.7 + - + +
308B LYS 2.8 17.1 + - - +
309B GLN* 3.5 34.6 + - - +
311B VAL* 1.3 78.8 - - - +
313B GLU* 1.3 58.3 + - - +
314B GLN 3.2 0.2 - - - -
315B MET 3.5 1.2 + - - -
316B PHE* 3.0 54.5 + - + -
3401B O16 5.1 14.8 - - - -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLN 3.3 16.5 + - - +
310B ASP* 2.9 8.6 + - - +
312B LYS* 1.3 79.3 - - - +
314B GLN* 1.3 62.9 + - - +
316B PHE* 3.7 11.4 - - + -
317B ASN* 2.7 41.8 + - + +
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASP 3.0 12.9 + - - +
311B VAL* 3.6 13.0 - - + +
312B LYS 3.2 0.2 - - - -
313B GLU* 1.3 83.7 + - - +
315B MET* 1.3 81.1 + - + +
317B ASN* 4.4 3.4 - - - +
318B GLU* 2.5 52.4 + - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B PRO* 3.8 28.0 - - + -
311B VAL* 2.9 35.7 - - + +
312B LYS 3.5 1.5 + - - +
314B GLN* 1.3 94.8 - - + +
316B PHE* 1.3 66.4 + - - +
318B GLU* 3.4 8.5 + - + +
319B LEU* 2.9 34.3 + - + +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PHE* 3.7 25.8 - + + -
303B PRO* 3.6 39.7 - - + -
304B TRP* 3.8 29.8 - + - -
312B LYS* 3.0 45.4 + - + +
313B GLU* 3.7 11.7 - - + +
315B MET* 1.3 77.1 - - - +
317B ASN* 1.3 58.9 + - - +
319B LEU* 3.1 2.1 + - - +
320B LEU* 2.8 45.4 + - + +
363B PHE* 3.9 33.7 - + - -
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B GLU* 2.7 36.7 + - + +
314B GLN* 3.7 7.0 - - - +
316B PHE* 1.3 73.7 - - - +
318B GLU* 1.3 66.8 + - - +
320B LEU* 4.7 3.6 - - - -
321B THR* 2.7 61.7 + - - +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLN* 2.5 50.7 + - - +
315B MET* 3.8 9.7 - - + +
316B PHE 3.3 0.2 - - - -
317B ASN* 1.3 93.2 - - - +
319B LEU* 1.3 57.9 + - + +
321B THR* 4.7 0.8 - - - -
322B TYR* 3.0 55.5 + - + +
323B ASN* 3.3 6.3 - - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B PHE* 3.7 10.9 - - + -
301B CYS* 3.7 42.6 - - + +
302B PHE* 3.8 37.7 - - + -
303B PRO* 4.3 2.0 - - + -
315B MET* 2.9 30.3 + - + +
316B PHE 3.5 3.1 - - - +
318B GLU* 1.3 77.5 - - + +
320B LEU* 1.3 55.4 + - - +
323B ASN* 3.3 28.9 + - - +
324B ALA* 2.8 33.3 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PHE* 3.2 34.5 - - + -
316B PHE* 2.8 47.0 + - + +
317B ASN* 3.9 3.8 - - - +
319B LEU* 1.3 74.7 - - - +
321B THR* 1.3 56.1 + - - +
324B ALA* 3.2 23.2 - - + +
325B PRO* 3.3 0.2 - - - +
360B LEU* 4.2 20.2 - - + +
363B PHE* 4.3 16.4 - - + +
364B LYS* 2.7 55.6 + - + +
367B LEU* 5.4 1.6 - - + -
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASN* 2.7 45.0 + - - +
318B GLU* 4.5 1.6 - - - -
320B LEU* 1.3 76.5 - - - +
322B TYR* 1.3 87.0 + - + +
325B PRO* 3.5 14.7 - - - +
364B LYS* 3.8 7.9 + - - +
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Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B GLU* 3.0 37.9 + - + +
321B THR* 1.3 103.5 - - + +
323B ASN* 1.3 68.2 + - - +
324B ALA 3.4 0.7 - - - -
325B PRO* 3.1 9.9 - - - +
326B HIS* 2.9 32.9 + - - +
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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