Contacts of the helix formed by residues 430 - 438 (chain B) in PDB entry 5U3W
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 HIS 430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A PHE* 5.0 7.7 - + - -
365A MET* 5.3 3.1 - - + -
250B GLN* 2.8 31.6 + - + +
251B CME 3.5 31.1 + - + +
254B VAL* 3.7 24.5 - - + +
428B SER 4.0 0.2 - - - -
429B LEU* 1.3 72.6 - - - +
431B PRO* 1.3 83.8 - - + +
432B LEU* 3.0 44.2 + - + +
433B LEU* 3.1 20.1 + - + +
434B GLN* 3.1 10.2 + - - +
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Residues in contact with PRO 431 (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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365A MET* 3.9 27.6 - - + +
429B LEU 3.5 5.6 - - - +
430B HIS* 1.3 99.9 - - + +
432B LEU* 1.3 61.6 + - - +
434B GLN* 3.2 8.8 + - + +
435B GLU* 3.1 26.7 + - - +
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Residues in contact with LEU 432 (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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274A PHE* 3.4 39.3 - - + -
276A ASN* 3.4 35.4 - - - +
365A MET* 3.7 14.0 - - + -
501A B7G 4.2 12.3 - - + -
254B VAL* 4.2 13.0 - - + -
257B VAL* 4.0 22.7 - - + -
430B HIS* 3.0 19.8 + - + +
431B PRO* 1.3 78.4 - - - +
433B LEU* 1.3 64.2 + - + +
435B GLU* 3.2 13.6 + - - +
436B ILE* 3.2 19.4 + - + +
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Residues in contact with LEU 433 (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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250B GLN* 3.5 31.6 - - + +
253B THR* 3.6 25.4 - - + -
254B VAL* 4.0 18.4 - - + +
257B VAL* 5.1 3.6 - - + -
287B HIS* 4.3 9.0 - - + +
429B LEU* 6.1 1.3 - - + -
430B HIS* 3.1 10.8 + - + +
432B LEU* 1.3 77.8 - - + +
434B GLN* 1.3 57.4 + - - +
436B ILE* 3.2 18.2 + - + +
437B TYR* 3.0 45.0 + - + -
501B 7U1 3.5 33.7 - - + +
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Residues in contact with GLN 434 (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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418B GLN* 3.8 13.9 + - - -
421B LYS* 3.4 41.8 - - - +
429B LEU* 3.7 32.3 + - + +
430B HIS 3.1 11.2 + - - +
431B PRO* 3.5 12.3 - - + +
432B LEU 3.2 0.2 - - - -
433B LEU* 1.3 72.9 - - - +
435B GLU* 1.3 62.9 + - + +
437B TYR* 3.3 6.5 + - - +
438B LYS* 2.9 35.3 + - + +
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Residues in contact with GLU 435 (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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276A ASN* 4.1 16.8 - - - +
363A GLY 5.0 8.6 - - - +
365A MET* 4.4 13.6 - - + +
501A B7G 3.0 49.1 + - + +
283B LYS* 3.9 1.7 - - - -
431B PRO* 3.1 17.0 + - - +
432B LEU 3.2 8.2 + - - +
434B GLN* 1.3 80.6 - - - +
436B ILE* 1.3 61.8 + - - +
438B LYS* 3.0 40.8 + - - +
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Residues in contact with ILE 436 (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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501A B7G 3.5 26.0 - - + -
257B VAL* 4.7 6.5 - - + -
283B LYS* 3.2 44.4 - - - +
286B VAL* 4.0 21.3 - - + -
287B HIS* 3.8 29.4 - - + +
432B LEU* 3.2 21.7 + - + +
433B LEU* 3.2 20.5 + - + +
435B GLU* 1.3 79.2 - - - +
437B TYR* 1.3 61.6 + - + +
438B LYS 3.5 0.2 + - - -
439B ASP 4.4 0.2 + - - -
440B MET* 3.7 17.5 - - + +
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Residues in contact with TYR 437 (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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287B HIS* 2.8 25.7 + + - -
410B VAL* 6.1 1.1 - - + -
413B HIS* 2.8 21.6 + + - -
414B ALA* 4.1 26.2 - - + -
417B MET* 3.8 25.4 - - + -
418B GLN* 3.8 29.1 + - + +
433B LEU* 3.0 33.0 + - + +
434B GLN* 4.0 7.9 - - - +
436B ILE* 1.3 76.5 - - + +
438B LYS* 1.3 66.3 + - - +
439B ASP 3.0 2.9 + - - -
440B MET* 3.2 26.5 + - - +
501B 7U1 2.7 42.0 + - - -
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Residues in contact with LYS 438 (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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501A B7G 3.0 32.0 + - - -
418B GLN* 5.8 0.9 - - - +
434B GLN* 2.9 21.2 + - + +
435B GLU* 3.0 35.9 + - - +
436B ILE 3.3 1.0 - - - -
437B TYR* 1.3 77.0 - - - +
439B ASP* 1.3 74.5 + - - +
440B MET 3.8 2.6 + - - +
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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
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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