Contacts of the helix formed by residues 427 - 435 (chain a) in PDB entry 5W97
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 PRO 427 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422a ASN 3.9 0.2 - - - +
423a MET* 3.1 25.8 - - - +
424a THR 3.9 3.6 - - - +
425a PHE 3.5 3.1 - - - -
426a PHE* 1.3 96.3 - - + +
428a GLN* 1.3 57.7 + - - +
430a PHE* 2.9 34.8 + - + +
431a LEU* 3.2 14.0 + - - +
450a TRP* 4.1 37.5 - - + +
453a ILE* 4.3 16.4 - - + -
454a SER* 4.9 1.8 - - - +
101i TGL 5.1 7.6 - - + -
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Residues in contact with GLN 428 (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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38a ARG* 3.3 6.6 - - - +
371a TYR* 3.6 36.9 - - + +
374a VAL* 3.5 18.2 - - - +
375a ALA* 4.1 5.1 + - + -
424a THR* 3.5 12.4 + - - +
425a PHE* 3.1 36.5 + - - +
427a PRO* 1.3 75.7 - - - +
429a HIS* 1.3 60.4 + - - +
431a LEU* 3.3 17.1 + - + +
432a GLY 2.9 19.4 + - - -
454a SER* 3.2 22.1 + - - +
601a HEA 3.3 24.0 + - - -
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Residues in contact with HIS 429 (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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350a VAL* 5.0 4.0 - - + +
354a THR* 3.9 29.9 + - + +
372a TYR* 3.8 19.1 - + + +
375a ALA* 3.7 22.3 - - + +
379a TYR* 3.6 34.7 - + - -
425a PHE 3.9 0.2 + - - -
426a PHE* 2.8 38.5 + + + +
427a PRO 3.1 0.6 - - - -
428a GLN* 1.3 78.0 - - - +
430a PHE* 1.3 59.4 + - + +
432a GLY* 3.4 1.0 + - - -
433a LEU* 3.0 34.1 + - - +
101i TGL 4.0 32.9 - - + +
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Residues in contact with PHE 430 (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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426a PHE* 3.5 34.5 - + - -
427a PRO* 2.9 29.7 + - + +
429a HIS* 1.3 72.6 - - + +
431a LEU* 1.3 68.7 + - - +
433a LEU* 3.3 1.9 + - - +
434a SER* 2.8 28.0 + - - -
450a TRP* 3.8 30.7 - + + +
6b GLN 3.5 17.7 - - - +
7b LEU* 3.2 48.5 - - + +
101i TGL 3.8 48.9 - - + -
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Residues in contact with LEU 431 (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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38a ARG* 5.5 0.2 - - - +
371a TYR* 3.9 12.3 - - + -
427a PRO 3.2 2.6 + - - +
428a GLN* 3.5 29.8 - - + +
430a PHE* 1.3 77.7 - - - +
432a GLY* 1.3 58.0 + - - +
434a SER* 2.8 18.2 + - - -
435a GLY 2.8 15.4 + - - -
436a MET* 3.1 20.5 + - + -
447a TYR* 3.7 25.1 - - + +
450a TRP* 3.7 33.8 - - + +
451a ASN* 3.4 44.2 - - - +
454a SER* 5.4 1.1 - - - -
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Residues in contact with GLY 432 (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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366a VAL 4.9 1.9 - - - +
367a LEU* 4.8 3.8 - - - +
370a THR* 3.6 19.8 - - - +
371a TYR* 3.8 7.0 - - - +
372a TYR* 3.4 28.5 - - - -
428a GLN 2.9 11.7 + - - -
429a HIS 3.7 1.6 - - - -
431a LEU* 1.3 75.5 - - - +
433a LEU* 1.3 61.9 + - - +
435a GLY* 3.0 15.1 + - - -
436a MET 4.4 0.7 - - - -
9b PHE* 5.3 0.3 - - - -
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Residues in contact with LEU 433 (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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367a LEU* 4.0 4.5 - - + -
372a TYR* 3.8 20.3 - - + -
429a HIS 3.0 20.4 + - - +
430a PHE 3.9 1.8 - - - +
432a GLY* 1.3 76.3 - - - +
434a SER* 1.3 60.5 + - - +
435a GLY* 3.4 0.9 + - - -
7b LEU 3.5 13.9 - - - +
8b GLY* 3.5 18.6 - - - -
9b PHE* 3.2 56.7 - - + +
10b GLN 4.3 0.9 + - - -
24b HIS* 3.7 21.3 - - + +
166b PRO* 6.2 0.2 - - - +
101i TGL 3.0 39.3 - - + +
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Residues in contact with SER 434 (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 PHE 2.8 21.0 + - - -
431a LEU* 2.8 21.0 + - - +
433a LEU* 1.3 71.6 - - - +
435a GLY* 1.3 56.7 + - - +
447a TYR* 3.0 28.0 + - - -
450a TRP* 5.5 1.2 - - - -
2b ALA* 3.6 2.6 - - - +
6b GLN* 3.7 38.5 + - - -
8b GLY 3.4 8.5 + - - -
10b GLN* 2.9 26.8 + - - +
166b PRO* 5.9 0.4 - - - -
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Residues in contact with GLY 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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366a VAL 5.9 1.1 - - - -
370a THR* 5.0 7.7 - - - +
431a LEU 2.8 6.5 + - - -
432a GLY 3.0 11.4 + - - -
433a LEU 3.2 1.5 - - - -
434a SER* 1.3 78.5 - - - +
436a MET* 1.3 63.3 + - - -
437a PRO* 3.1 12.0 - - - +
447a TYR* 3.5 8.8 + - - -
10b GLN* 4.6 4.5 - - - -
166b PRO* 4.8 16.3 - - - +
195b GLN* 4.5 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