Contacts of the strand formed by residues 438 - 445 (chain A) in PDB entry 5DQE
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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A PHE* 3.5 3.6 - - - -
303A TRP* 2.8 48.3 + - + +
435A ARG* 3.2 29.0 + - - +
436A GLY 4.4 4.7 - - - +
437A ALA* 1.3 78.3 - - - +
439A HIS* 1.3 78.2 + - - +
440A HIS* 3.7 27.2 + - + +
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Residues in contact with HIS 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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253A HIS 3.4 24.1 + - - -
254A ILE* 4.0 29.0 - - + +
255A SER 5.1 2.3 + - - -
256A GLN* 5.4 1.6 - - - -
300A VAL* 4.2 4.5 - - + -
301A LYS 3.0 11.7 - - - +
302A PHE* 3.5 20.2 - + + -
303A TRP* 4.2 0.4 - - - -
438A GLN* 1.3 83.6 - - + +
440A HIS* 1.3 80.9 + - - +
441A ILE* 3.9 24.9 + - + +
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Residues in contact with HIS 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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300A VAL* 3.5 1.2 - - - -
301A LYS* 2.9 32.7 + - + -
303A TRP* 3.6 28.9 - + + -
438A GLN* 3.7 27.4 + - + -
439A HIS* 1.3 83.4 + - - +
441A ILE* 1.3 63.0 + - - +
442A TYR* 3.1 39.9 - - + +
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Residues in contact with ILE 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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222A GLY* 5.0 1.6 - - - -
223A LEU* 4.1 35.4 - - + +
254A ILE* 4.6 5.4 - - + -
256A GLN* 3.7 26.5 - - - +
266A LEU* 4.0 29.3 - - + +
267A GLU 4.5 2.4 + - - +
298A PHE* 4.2 15.7 - - + -
299A LEU 3.5 6.5 - - - +
300A VAL* 4.2 14.8 - - + -
439A HIS* 3.9 25.8 + - + +
440A HIS* 1.3 76.1 - - - +
442A TYR* 1.3 73.2 + - - +
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Residues in contact with TYR 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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266A LEU* 4.5 1.6 - - - -
267A GLU* 3.5 48.8 + - + +
269A VAL* 3.7 28.5 - - + -
298A PHE* 3.2 12.6 - - - +
299A LEU* 2.7 52.6 + - + +
301A LYS* 4.5 11.2 - - + -
303A TRP* 5.2 3.3 - - - -
440A HIS* 3.1 56.8 - + + +
441A ILE* 1.3 79.2 - - - +
443A ARG* 1.3 60.1 + - - +
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Residues in contact with ARG 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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266A LEU* 2.4 48.1 + - + +
267A GLU 3.2 9.1 + - - +
268A SER* 3.7 18.6 - - - -
269A VAL* 2.8 28.1 + - - +
295A HIS* 5.6 9.0 - - - +
297A PHE 3.9 5.6 - - - +
298A PHE* 4.0 22.7 - - + -
442A TYR* 1.3 76.6 - - - +
444A LEU* 1.3 63.2 + - - +
445A VAL* 4.7 11.0 - - + +
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Residues in contact with LEU 444 (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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269A VAL* 3.3 24.7 - - + +
271A VAL* 4.1 13.9 - - + -
274A ILE* 4.4 17.0 - - + -
285A LEU* 3.8 29.4 - - + -
289A TYR* 3.1 15.8 + - - -
294A PRO 3.9 9.2 - - - +
297A PHE* 2.9 29.9 + - + +
298A PHE 4.0 23.3 - - - +
299A LEU* 3.7 23.1 - - + -
423A CYS* 5.7 0.9 - - - +
425A ALA* 4.9 4.7 - - + +
443A ARG* 1.3 72.2 - - - +
445A VAL* 1.3 67.3 + - - +
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Residues in contact with VAL 445 (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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268A SER* 3.1 30.7 - - - +
269A VAL 2.9 9.3 + - - +
270A ASP* 3.1 11.8 - - + +
271A VAL* 2.7 34.6 + - - +
289A TYR* 3.4 7.9 - - - +
443A ARG* 4.7 13.2 - - + +
444A LEU* 1.3 80.4 - - - +
446A ARG* 1.3 64.8 + - - +
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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