Contacts of the helix formed by residues 398 - 403 (chain A) in PDB entry 1JV1
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 LEU 398 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ALA* 5.5 1.5 - - + +
81A THR* 3.6 26.5 - - + +
280A VAL* 4.3 0.7 - - - -
397A VAL* 1.3 77.9 - - - +
399A ARG* 1.3 67.0 + - - +
400A GLU* 3.7 17.9 - - - +
401A ASP* 3.1 34.3 + - - +
402A GLU* 3.2 13.8 + - - +
315B ARG* 3.4 42.4 - - - +
319B GLY 5.6 0.4 - - - +
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.9 1.7 - - - +
280A VAL* 3.7 32.3 - - + +
281A GLU 3.1 26.9 + - - -
282A LYS* 4.1 1.4 - - - +
283A THR* 4.6 6.4 + - - +
287A GLU* 2.8 43.2 + - - -
397A VAL 3.8 2.8 + - - -
398A LEU* 1.3 72.3 - - - +
400A GLU* 1.3 71.4 + - + +
403A PHE* 2.9 59.7 + - + +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.6 13.6 - - - +
398A LEU* 3.7 15.8 - - - +
399A ARG* 1.3 88.0 + - + +
401A ASP* 1.3 71.3 + - - +
424A ALA* 4.8 2.9 - - - +
428A LEU* 3.7 19.7 - - + +
283B THR 4.6 5.8 - - - +
284B ASN* 4.5 18.8 - - - +
285B PRO* 3.4 32.0 - - + +
313B GLN* 6.4 0.2 - - - +
315B ARG* 3.4 18.5 + - - -
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Residues in contact with ASP 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.1 11.1 - - - +
258A LYS* 4.8 6.6 - - + +
398A LEU* 3.1 35.5 + - + +
399A ARG 3.1 0.6 - - - -
400A GLU* 1.3 88.4 - - - +
402A GLU* 1.3 70.2 + - + +
428A LEU* 3.5 34.6 - - + +
432A TRP* 5.0 2.1 + - - -
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 5.8 0.3 - - - +
254A ASN* 3.0 18.7 + - - -
256A LEU* 3.6 17.2 - - - +
257A VAL* 4.4 1.7 - - - -
258A LYS* 3.2 37.0 + - + +
261A ASP* 4.4 1.7 - - - +
278A LYS* 2.8 31.4 + - - +
328A ILE* 4.2 7.4 - - + +
397A VAL* 3.3 41.1 - - + +
398A LEU 3.2 8.8 + - - +
399A ARG 3.2 0.4 + - - -
401A ASP* 1.3 95.1 - - + +
403A PHE* 1.3 61.0 + - + +
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Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASP* 5.6 0.4 - - - -
254A ASN* 3.6 14.4 - - + -
256A LEU* 3.6 2.2 - - - +
280A VAL* 4.1 16.4 - - + -
287A GLU* 3.9 20.9 - - - -
289A VAL* 4.1 10.3 - - + -
328A ILE* 3.5 41.5 - - + -
399A ARG* 2.9 45.8 + - + +
402A GLU* 1.3 75.3 - - - +
404A SER* 1.3 63.6 + - - +
405A PRO* 3.7 27.7 - - + +
901A UD1 3.5 36.6 - - - -
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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
------------------------------------------------------------
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