Contacts of the helix formed by residues 434 - 443 (chain A) in PDB entry 2JG7
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A ASP* 3.1 13.1 + - - +
432A THR* 3.4 10.6 + - - +
433A LYS* 1.3 74.9 - - - +
435A LEU* 1.3 64.4 + - - +
436A GLY* 3.0 8.4 + - - -
437A ARG* 2.7 50.9 + - + +
438A VAL* 3.1 24.1 + - - +
440A ARG* 4.1 5.6 + - - -
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Residues in contact with LEU 435 (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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433A LYS 3.4 6.0 + - - -
434A ASP* 1.3 72.9 + - - +
436A GLY* 1.3 61.3 + - - +
438A VAL* 3.4 12.7 + - - +
439A PHE* 3.4 42.9 - - + -
495C ILE* 4.7 8.3 - - + -
496C ASN 4.1 11.7 - - - +
497C TYR* 4.0 10.1 - - + -
432D THR 4.5 6.1 - - - +
433D LYS* 4.4 19.6 + - + +
435D LEU* 4.3 20.4 - - + +
438D VAL* 4.4 25.4 - - + -
439D PHE* 5.7 0.2 - - + -
455D ASN* 3.7 26.5 - - - +
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Residues in contact with GLY 436 (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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434A ASP* 3.0 6.7 + - - -
435A LEU* 1.3 76.3 - - - +
437A ARG* 1.3 64.1 + - - +
439A PHE* 3.4 2.3 + - - -
440A ARG* 3.0 41.5 + - - +
497C TYR* 3.2 32.0 + - - -
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Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 3.5 47.7 - - - +
278A GLU 5.2 0.4 - - - +
279A ASP* 3.5 13.1 + - - -
412A GLU* 2.8 31.9 + - - +
416A PHE* 4.3 4.0 - - + -
430A ILE* 4.0 9.6 - - + -
432A THR* 2.9 27.8 + - + -
434A ASP* 2.7 39.6 + - + +
436A GLY* 1.3 74.0 - - - +
438A VAL* 1.3 62.5 + - - +
440A ARG* 3.2 16.4 + - - +
441A TRP* 2.9 25.7 + - - +
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Residues in contact with VAL 438 (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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430A ILE* 4.4 4.0 - - - +
432A THR* 4.0 12.1 - - + +
434A ASP 3.1 16.6 + - - +
435A LEU* 3.5 9.2 - - - +
437A ARG* 1.3 76.2 - - - +
439A PHE* 1.3 69.9 + - + +
441A TRP* 3.3 8.1 - - - +
442A LEU* 3.1 29.0 + - + +
454A VAL* 3.8 37.2 - - + -
495B ILE* 4.4 22.7 - - + -
435D LEU* 4.3 19.7 - - + -
439D PHE* 6.0 0.2 - - + -
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Residues in contact with PHE 439 (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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435A LEU* 3.4 35.0 - - + -
436A GLY 3.4 1.8 + - - -
437A ARG 3.3 0.6 - - - -
438A VAL* 1.3 87.6 - - + +
440A ARG* 1.3 60.4 + - - +
442A LEU* 3.3 20.9 + - + +
443A GLY* 2.9 26.5 + - - -
150B ILE* 5.5 7.0 - - + -
152B GLN* 6.6 0.2 - - - -
495B ILE* 5.3 2.7 - - + -
148C ALA* 3.6 27.4 - - + -
150C ILE* 6.2 2.0 - - + -
495C ILE* 4.1 27.1 - - + -
497C TYR* 3.6 45.0 + + + -
439D PHE* 4.5 19.3 - + - -
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Residues in contact with ARG 440 (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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412A GLU* 2.8 46.2 + - - +
416A PHE* 4.3 4.3 - - + -
434A ASP* 4.1 4.9 + - - -
436A GLY* 3.0 37.0 + - - +
437A ARG* 3.3 23.4 - - - +
439A PHE* 1.3 77.8 - - - +
441A TRP* 1.3 62.4 + - - +
443A GLY* 3.2 12.5 + - - -
445A LYS* 3.9 4.3 + - + +
446A GLY* 3.3 18.8 + - - -
497C TYR* 4.7 12.9 + - + -
498C SER* 6.1 0.6 - - - +
499C LYS* 4.4 24.4 - - - +
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Residues in contact with TRP 441 (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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275A ILE* 4.0 8.5 - - + -
416A PHE* 3.5 36.9 - + + -
419A ASN* 3.7 21.5 - - + -
428A SER* 3.4 27.4 - - - -
429A SER 3.8 9.0 - - - -
430A ILE* 3.4 43.0 - - + +
437A ARG 2.9 17.2 + - - +
438A VAL 3.3 3.6 - - - +
440A ARG* 1.3 77.6 - - - +
442A LEU* 1.3 60.7 + - + +
446A GLY* 3.4 3.5 - - - -
447A SER* 3.1 52.8 + - - +
452A VAL* 3.3 27.4 - - + +
453A ASN 3.0 18.0 + - - +
454A VAL* 3.7 16.8 - - + -
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Residues in contact with LEU 442 (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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438A VAL* 3.1 21.6 + - + +
439A PHE* 3.7 21.1 - - + +
440A ARG 3.2 0.2 - - - -
441A TRP* 1.3 81.9 - - + +
443A GLY* 1.3 61.1 + - - +
447A SER 5.6 0.6 - - - +
452A VAL* 3.7 34.7 - - + +
454A VAL* 4.3 8.1 - - + -
150B ILE* 4.0 18.2 - - + -
152B GLN* 3.4 19.7 + - + +
154B ASN* 3.1 19.9 + - - -
491B SER* 4.7 2.6 + - - -
493B CYS* 4.0 18.2 - - + -
495B ILE* 3.7 28.3 - - + -
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Residues in contact with GLY 443 (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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439A PHE 2.9 16.9 + - - -
440A ARG* 3.2 4.9 + - - -
441A TRP 4.1 0.5 - - - +
442A LEU* 1.3 80.6 - - - +
444A PRO* 1.4 70.4 - - - +
445A LYS 3.3 2.5 - - - -
446A GLY* 3.2 18.4 + - - -
447A SER 4.6 0.7 - - - +
152B GLN* 4.5 5.2 - - - -
154B ASN* 3.3 12.3 + - - -
489B ARG* 3.9 5.0 + - - -
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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