Contacts of the helix formed by residues 395 - 403 (chain A) in PDB entry 5MQI
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 ARG 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A GLU* 4.1 14.6 + - - -
389A ASN* 3.2 14.4 + - - -
393A SER 3.9 0.2 + - - -
394A PHE* 1.3 74.1 - - - +
396A PRO* 1.3 76.6 - - + +
397A GLY* 3.1 22.9 + - - +
398A LEU* 3.2 41.3 + - + +
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Residues in contact with PRO 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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389A ASN* 4.4 6.5 - - - +
394A PHE 3.6 4.0 - - - +
395A ARG* 1.3 88.2 - - + +
397A GLY* 1.3 63.0 + - - +
398A LEU 3.1 0.4 - - - -
399A VAL* 3.1 21.5 + - + +
400A SER* 3.4 9.6 + - - -
403A LEU* 4.5 17.6 - - + +
453A MET* 5.8 8.3 - - + -
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Residues in contact with GLY 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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355A ASN* 3.0 20.4 + - - -
395A ARG* 3.1 23.0 - - - +
396A PRO* 1.3 80.8 - - - +
398A LEU* 1.3 58.1 + - - +
400A SER* 3.2 17.9 + - - -
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Residues in contact with LEU 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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350A LEU* 3.7 35.0 - - + +
351A GLU* 3.6 32.5 - - - +
354A TYR* 3.5 12.5 - - - +
355A ASN* 3.2 18.9 + - - +
389A ASN* 3.7 23.3 - - - +
394A PHE* 3.9 23.8 - - + -
395A ARG* 3.6 44.0 - - + +
396A PRO 3.1 1.6 - - - -
397A GLY* 1.3 76.9 - - - +
399A VAL* 1.3 57.6 + - - +
400A SER 3.6 0.2 - - - -
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Residues in contact with VAL 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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350A LEU* 3.7 23.1 - - + -
354A TYR* 3.8 17.7 - - + -
355A ASN* 3.4 3.1 - - - -
386A MET* 4.0 33.7 - - + -
389A ASN* 3.9 26.9 - - + +
396A PRO* 3.1 13.0 + - + +
398A LEU* 1.3 81.0 - - - +
400A SER* 1.3 64.5 + - - +
401A GLU 3.1 4.0 - - - -
402A THR* 2.9 15.2 + - - -
403A LEU* 3.1 19.6 + - + +
449A THR* 5.7 1.6 - - + -
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Residues in contact with SER 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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355A ASN* 3.2 10.6 + - - -
396A PRO 3.4 5.0 + - - -
397A GLY* 3.2 25.2 + - - -
399A VAL* 1.3 78.0 - - - +
401A GLU* 1.3 64.9 + - - +
403A LEU* 3.1 25.2 + - - +
404A SER* 4.3 5.2 - - - -
406A ARG* 5.9 0.3 + - - -
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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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354A TYR* 5.3 0.4 - - + -
355A ASN* 2.9 45.6 + - + +
358A MET* 4.2 10.3 - - + +
359A GLY* 3.7 27.5 - - - +
362A LYS* 4.5 17.7 + - - +
378A TYR* 5.1 1.9 + - - -
400A SER* 1.3 80.1 + - - +
402A THR* 1.3 59.6 + - + +
404A SER* 4.2 3.5 + - - -
406A ARG* 5.4 7.7 + - - -
407A THR* 3.4 10.6 + - - -
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Residues in contact with THR 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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354A TYR* 2.8 35.7 + - + +
358A MET* 4.0 20.4 - - + -
378A TYR* 3.7 22.2 - - - +
382A LEU* 4.0 16.2 - - + -
386A MET* 3.2 11.7 - - - +
399A VAL 2.9 7.6 + - - -
401A GLU* 1.3 80.1 - - + +
403A LEU* 1.3 59.3 + - - +
407A THR* 3.3 13.8 - - - +
446A LEU* 3.3 24.1 - - - +
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Residues in contact with LEU 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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386A MET* 4.0 8.7 - - + -
396A PRO* 4.5 20.9 - - + +
399A VAL* 3.1 27.2 + - + +
400A SER* 3.1 14.4 + - - +
401A GLU 3.5 0.2 - - - -
402A THR* 1.3 80.0 - - - +
404A SER* 1.3 61.2 + - - +
408A PHE* 5.3 1.8 - - + -
446A LEU* 5.0 5.8 - - + -
449A THR* 3.8 33.4 - - + -
450A VAL* 4.0 22.7 - - + -
453A MET* 4.6 17.9 - - + -
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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