Contacts of the helix formed by residues 394 - 403 (chain A) in PDB entry 4U7D
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 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A SER* 3.3 4.1 + - - -
393A LYS* 1.3 82.1 - - - +
395A MET* 1.3 66.0 + - - +
396A GLU* 3.4 16.6 + - - +
397A ASN* 3.0 32.1 + - - +
398A TYR* 2.9 21.8 + - - +
439A LYS* 3.8 33.1 + - - +
443A MET* 4.4 7.0 - - - -
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Residues in contact with MET 395 (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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394A SER* 1.3 71.9 - - - +
396A GLU* 1.3 59.0 + - - +
398A TYR* 3.2 3.8 + - + +
399A TYR* 3.0 31.8 + - - +
439A LYS 4.5 2.4 + - - -
442A GLU* 4.1 4.7 - - + +
443A MET* 3.4 40.9 - - + +
446A TYR* 3.5 30.7 - - + -
457A LEU* 5.8 1.6 - - - +
458A MET* 3.7 40.8 - - + -
461A HIS* 3.4 46.8 - - + +
462A PHE* 5.3 4.2 - - + -
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Residues in contact with GLU 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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256A THR* 6.6 0.4 - - + -
394A SER* 3.4 20.0 - - - +
395A MET* 1.3 80.6 + - - +
397A ASN* 1.3 63.7 + - - +
399A TYR* 3.8 6.0 + - - +
400A GLN* 3.3 25.6 + - - +
439A LYS* 4.5 10.1 - - - +
461A HIS* 2.8 37.0 + - - +
462A PHE* 5.0 18.5 - - + -
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Residues in contact with ASN 397 (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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372A VAL* 4.9 6.5 - - - +
392A SER* 4.0 7.6 - - - -
393A LYS* 3.4 35.5 - - - +
394A SER* 3.0 25.8 + - - +
396A GLU* 1.3 78.7 - - - +
398A TYR* 1.3 59.8 + - - +
400A GLN* 3.8 9.6 - - - +
401A GLU* 2.8 53.4 + - - +
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Residues in contact with TYR 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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288A TYR* 4.3 6.7 - + - -
289A GLU 4.5 1.7 + - - -
386A VAL 5.4 0.2 + - - -
388A HIS* 3.1 46.4 + + - -
392A SER* 3.6 13.0 + - - +
394A SER 2.9 13.3 + - - +
395A MET* 3.2 8.5 + - + +
397A ASN* 1.3 77.0 - - - +
399A TYR* 1.3 53.5 - - - +
401A GLU* 2.9 2.4 + - - +
402A SER* 2.6 54.9 + - - -
414A CYS* 3.6 28.6 + - - +
415A ILE 4.4 0.5 + - - -
416A LEU* 3.7 33.2 + - + +
443A MET* 4.2 14.1 - - + -
446A TYR* 4.2 23.9 + + - -
458A MET* 3.9 17.7 - - + -
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Residues in contact with TYR 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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114A PRO* 3.0 35.8 - - + +
115A THR 5.3 1.8 - - - -
281A PHE* 2.4 55.3 + + + -
283A ARG* 4.2 11.5 - - + +
288A TYR* 4.3 11.7 - - - -
395A MET 3.0 16.6 + - - +
396A GLU* 4.0 4.3 - - - +
398A TYR* 1.3 76.0 - - - +
400A GLN* 1.3 62.7 + - + +
402A SER* 3.2 5.7 + - - -
403A GLY* 2.7 35.8 + - - -
458A MET* 4.0 24.2 - - + -
462A PHE* 4.0 26.0 - + + -
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Residues in contact with GLN 400 (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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115A THR* 3.7 31.0 + - - +
255A ALA* 5.2 2.0 - - + +
256A THR* 4.6 22.6 - - - +
396A GLU 3.3 17.4 + - - +
397A ASN* 3.9 10.5 - - - +
398A TYR 3.1 0.4 - - - -
399A TYR* 1.3 88.0 - - + +
401A GLU* 1.3 63.5 + - + +
403A GLY* 3.5 5.1 + - - -
404A ARG* 3.3 39.5 + - - +
407A ARG* 5.1 1.4 + - - -
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Residues in contact with GLU 401 (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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320A TYR* 3.4 29.4 - - + +
372A VAL* 3.1 33.0 - - + +
386A VAL* 4.1 2.9 - - - +
388A HIS* 2.8 18.1 + - - +
392A SER* 2.4 28.9 + - - -
397A ASN* 2.8 36.6 + - - +
398A TYR 3.5 2.5 - - - +
400A GLN* 1.3 79.8 - - + +
402A SER* 1.3 60.7 + - - +
404A ARG* 3.3 37.8 + - - +
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Residues in contact with SER 402 (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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286A LEU* 4.2 2.2 - - - +
288A TYR* 4.0 9.4 + - - -
386A VAL* 4.0 12.5 - - - +
388A HIS* 4.1 2.4 - - - -
398A TYR* 2.6 54.8 + - - -
399A TYR* 3.2 10.4 + - - -
401A GLU* 1.3 70.5 - - - +
403A GLY* 1.3 60.8 + - - +
404A ARG 3.1 5.4 - - - -
405A ALA* 3.2 23.6 + - - +
414A CYS* 3.8 21.5 - - - -
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Residues in contact with GLY 403 (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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115A THR 5.7 0.4 - - - -
283A ARG* 2.7 37.2 + - - -
286A LEU* 4.5 7.4 - - - -
288A TYR* 5.4 0.9 - - - -
399A TYR* 2.7 25.0 + - - -
400A GLN* 4.0 3.6 - - - -
401A GLU 3.2 0.8 - - - -
402A SER* 1.3 76.4 - - - +
404A ARG* 1.3 59.2 + - - +
405A ALA 3.2 4.6 + - - -
407A ARG* 3.6 10.6 + - - -
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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