Contacts of the helix formed by residues 391 - 395 (chain B) in PDB entry 4YVE
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 GLN 391 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ALA* 3.9 27.3 - - + +
39B TYR* 4.2 15.9 - - + +
40B ASP* 2.8 24.7 + - - +
109B LYS* 3.4 19.2 - - - +
144B GLN* 4.9 4.6 + - - +
145B ASP 2.9 29.1 + - - -
146B ASP* 3.2 24.2 - - - +
381B PHE* 5.7 2.8 - - - -
390B ASN* 1.3 77.3 - - - +
392B LEU* 1.4 63.2 + - - +
393B PRO* 3.5 0.7 - - - -
394B PHE* 3.2 20.2 + - - +
395B VAL* 3.8 8.1 + - - +
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Residues in contact with LEU 392 (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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37A LEU* 3.8 21.5 - - + -
41A LEU* 4.2 6.5 - - + -
51A ASN 3.9 8.3 - - - +
52A ILE* 4.0 23.6 - - + -
55A PHE* 3.6 49.2 - - + -
58A ARG* 3.3 9.2 + - - -
36B ALA* 5.5 3.8 - - + -
37B LEU* 6.1 0.4 - - + -
40B ASP* 3.7 3.8 + - - +
387B PHE* 4.2 10.5 - - + -
389B GLY* 3.2 30.1 + - - +
391B GLN* 1.4 75.6 - - - +
393B PRO* 1.4 61.7 - - + +
394B PHE 2.8 7.1 + - - -
395B VAL* 3.1 21.0 + - + +
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Residues in contact with PRO 393 (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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51A ASN* 3.7 28.5 - - - +
54A ASN* 5.9 5.8 - - + +
55A PHE* 5.9 2.2 - - + +
58A ARG* 3.7 14.0 + - - +
113B ILE* 3.7 8.5 - - + -
118B SER* 4.1 23.0 - - - +
121B PHE* 3.5 18.4 - - - -
122B TRP* 3.7 6.8 + - - -
389B GLY 3.8 4.9 - - - +
390B ASN 3.3 16.4 - - - +
391B GLN 3.6 0.7 - - - -
392B LEU* 1.4 89.0 - - + +
394B PHE* 1.3 65.9 + - + -
395B VAL 3.7 0.2 - - - -
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Residues in contact with PHE 394 (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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58A ARG* 4.2 0.7 - - - +
109B LYS* 3.6 39.5 - - + -
112B MET* 3.8 23.1 - - + -
113B ILE* 3.9 26.9 - - + -
118B SER* 4.6 6.7 - - - -
121B PHE* 3.7 27.4 - + - -
122B TRP* 4.7 4.5 - - - -
144B GLN* 2.8 43.7 + - - +
149B LEU* 3.7 17.7 - - + -
381B PHE* 6.2 0.2 - + - -
390B ASN 3.4 21.5 - - - -
391B GLN* 3.2 15.7 + - - +
392B LEU 2.8 3.8 + - - -
393B PRO* 1.3 76.7 - - + +
395B VAL* 1.3 64.5 + - - +
396B GLY 3.2 0.5 + - - -
397B PHE* 3.3 8.0 + - - +
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Residues in contact with VAL 395 (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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34A LEU* 4.8 4.3 - - + -
37A LEU* 6.0 0.2 - - + -
55A PHE* 3.7 25.4 - - + -
58A ARG* 2.9 29.7 + - - +
59A TYR* 3.1 17.5 + - + +
29B CYS 4.1 4.5 - - - +
32B ASP* 4.4 5.2 - - - +
33B GLY* 3.6 27.8 - - - +
36B ALA* 3.7 29.8 - - + -
122B TRP* 3.6 2.3 - - - -
144B GLN* 5.2 0.2 - - - -
391B GLN 3.8 4.0 + - - +
392B LEU* 3.1 23.3 + - + +
394B PHE* 1.3 75.0 - - - +
396B GLY* 1.3 60.2 + - - +
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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