Contacts of the helix formed by residues 307 - 313 (chain B) in PDB entry 4V1M
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 ASP 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B CYS* 4.2 3.6 - - - -
304B ASP* 3.0 30.8 + - + +
306B ASN* 1.4 67.4 - - - +
308B TRP* 1.3 62.0 + - - +
309B GLN* 3.4 5.9 + - - +
310B MET* 3.2 35.5 + - - +
311B LEU* 3.3 26.1 + - - +
392B ARG* 3.0 36.0 + - - -
52I ILE* 4.6 5.4 - - - +
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Residues in contact with TRP 308 (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 ASN 2.7 15.2 + - - +
307B ASP* 1.3 70.3 - - - +
309B GLN* 1.3 90.5 + - + +
311B LEU* 3.2 8.7 + - - +
312B GLU* 2.8 41.9 + - + +
2I THR* 3.5 29.2 - - - -
3I THR* 3.7 28.3 - - - +
4I PHE* 5.9 2.5 - - + -
45I ARG* 3.1 53.4 - - + -
46I HIS 4.2 2.9 - - - -
47I GLU* 3.4 32.3 - - + -
52I ILE* 3.9 17.2 - - + +
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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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307B ASP* 3.5 9.6 - - - +
308B TRP* 1.3 105.4 - - + +
310B MET* 1.4 59.7 - - - +
312B GLU* 3.6 4.6 + - - +
313B MET* 3.5 17.8 + - - +
390B LEU* 3.7 27.6 - - + +
392B ARG* 3.2 20.3 + - - +
46I HIS 5.6 2.9 - - - +
47I GLU* 3.6 15.7 + - - +
50I THR* 3.5 21.4 + - - +
52I ILE* 3.4 37.1 - - + +
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Residues in contact with MET 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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301B ILE* 4.7 2.0 - - - +
302B CYS* 3.8 31.2 - - + -
307B ASP* 3.2 25.9 + - - +
309B GLN* 1.4 75.2 - - - +
311B LEU* 1.3 65.5 + - - +
313B MET* 3.1 18.8 - - - +
314B LEU* 3.4 11.0 + - + +
383B ASN* 3.7 40.2 - - - +
386B LEU* 3.8 30.1 - - + -
387B LEU* 3.8 23.6 - - + +
390B LEU* 3.9 17.7 - - + -
392B ARG* 4.1 1.7 - - - +
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Residues in contact with LEU 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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298B LEU* 3.8 36.8 - - + +
302B CYS* 4.1 21.3 - - + -
304B ASP 4.1 8.5 - - - +
305B VAL* 4.0 25.4 - - + +
307B ASP 3.3 21.4 + - - +
308B TRP* 3.2 8.4 + - - +
310B MET* 1.3 76.6 - - - +
312B GLU* 1.4 56.7 + - - +
314B LEU* 2.8 28.7 + - + +
315B LYS* 3.4 10.6 + - - +
4I PHE* 3.7 27.5 - - + -
6I PHE* 5.4 2.2 - - + -
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Residues in contact with GLU 312 (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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1261A LYS* 6.0 1.0 - - - -
308B TRP* 2.8 24.8 + - + +
309B GLN 3.9 6.3 - - - +
310B MET 3.4 0.2 - - - -
311B LEU* 1.4 69.7 - - - +
313B MET* 1.3 61.7 + - - +
315B LYS* 3.0 59.7 + - + +
316B PRO* 3.4 5.5 - - - +
2I THR* 3.4 28.2 + - - +
4I PHE* 4.9 1.0 - - - -
43I VAL 4.3 2.4 - - - +
44I TYR* 3.6 39.1 - - + +
45I ARG 3.9 6.8 + - - +
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Residues in contact with MET 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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258B LEU* 4.5 11.0 - - + -
267B ARG* 4.3 16.2 - - + +
269B ILE* 4.7 3.8 - - - +
309B GLN 3.5 6.5 + - - +
310B MET* 3.1 15.2 + - - +
311B LEU 3.1 0.2 - - - -
312B GLU* 1.3 78.2 - - - +
314B LEU* 1.3 57.6 + - - +
316B PRO* 3.5 18.0 - - - +
317B CYS* 4.3 6.2 - - - -
386B LEU* 3.5 31.2 - - + +
389B ALA* 3.7 27.8 - - + +
390B LEU* 3.7 36.1 - - + -
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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