Contacts of the strand formed by residues 395 - 399 (chain A) in PDB entry 2JI8
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 SER 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 5.5 1.0 - - - +
394A ILE* 1.3 77.2 - - - +
396A LEU* 1.3 59.4 + - - +
397A VAL 3.9 0.7 - - - -
417A ARG 4.9 1.9 + - - -
418A LYS* 3.5 22.9 + - - +
420A LEU* 4.4 6.3 - - - +
438A ALA* 3.9 28.5 - - - +
442A THR* 4.1 17.8 + - - +
445A PRO 3.2 11.0 + - - -
446A VAL* 3.5 7.6 - - - +
447A ILE* 2.8 28.2 + - - +
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Residues in contact with LEU 396 (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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384A VAL* 4.4 5.8 - - + -
388A MET* 4.2 19.3 - - + -
394A ILE 3.6 0.8 + - - -
395A SER* 1.3 71.2 - - - +
397A VAL* 1.3 73.1 + - - +
398A ASN* 4.0 14.3 + - + -
407A THR* 4.1 12.3 - - + -
411A VAL* 4.3 5.8 - - + -
413A MET* 3.6 33.4 - - + -
418A LYS 2.9 9.4 + - - -
419A ARG* 3.3 16.5 - - + +
420A LEU 2.9 24.8 + - - -
447A ILE* 3.3 32.5 - - + +
449A VAL* 4.4 9.6 - - + -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 1.3 76.0 - - - +
398A ASN* 1.3 67.5 + - - +
420A LEU* 3.4 25.1 - - + +
430A ILE* 4.5 3.6 - - + -
431A GLY* 3.6 26.5 - - - +
434A TYR* 3.9 23.6 - - + -
435A CYS* 4.0 7.9 - - - +
446A VAL* 4.0 22.0 - - + -
447A ILE 2.8 6.7 + - - +
448A ALA* 3.3 11.8 - - + -
449A VAL 2.9 24.7 + - - -
450A GLU* 3.7 15.5 - - - +
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Residues in contact with ASN 398 (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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396A LEU* 4.1 6.1 - - + +
397A VAL* 1.3 78.2 - - - +
399A GLU* 1.3 70.3 + - - +
403A ALA 3.0 20.7 + - - -
404A LEU* 3.4 10.1 - - - +
407A THR* 3.2 16.0 - - - -
419A ARG* 3.0 44.1 + - - +
420A LEU 3.1 6.9 + - - +
421A ASP* 3.1 29.4 - - + +
422A SER 3.5 0.9 + - - -
430A ILE* 3.9 2.8 - - - +
449A VAL* 2.7 35.2 + - - +
450A GLU* 4.7 0.2 - - - -
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Residues in contact with GLU 399 (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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398A ASN* 1.3 80.0 - - - +
400A GLY* 1.3 58.5 + - - +
403A ALA* 3.9 3.5 - - - +
404A LEU* 4.0 10.3 - - - -
422A SER* 3.2 17.3 - - - +
427A VAL 3.5 5.0 - - - +
428A MET* 3.5 3.5 - - + -
429A GLY 2.8 28.7 + - - -
430A ILE* 3.3 10.2 + - + +
431A GLY* 2.9 26.0 + - - -
449A VAL 3.5 4.9 + - - +
450A GLU* 2.5 33.1 - - - +
451A GLY 3.0 23.2 + - - -
454A ALA* 3.6 17.7 - - + +
458A SER* 4.4 1.7 + - - -
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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