Contacts of the helix formed by residues 331 - 336 (chain D) in PDB entry 4QGC
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 LEU 331 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D MET* 1.3 83.5 - - - +
332D GLU* 1.3 54.0 + - - +
333D SER 3.1 3.4 - - - -
334D MET* 2.8 45.2 + - + +
340D PRO* 4.0 21.1 - - + -
344D GLU* 3.7 13.7 - - + -
348D VAL* 3.9 15.5 - - + -
361D LEU* 3.9 16.6 - - + -
364D GLU* 3.0 28.3 + - + +
374D ALA* 3.8 23.3 - - - +
377D MET* 4.3 2.0 - - + -
378D GLN* 4.0 18.6 - - - +
381D ILE* 4.0 12.3 - - + -
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D THR* 4.6 1.6 - - - -
329D GLN* 3.3 45.1 + - + +
330D MET 3.7 0.2 - - - -
331D LEU* 1.3 75.6 - - - +
333D SER* 1.3 61.0 + - - +
335D ILE* 3.2 42.9 + - + +
344D GLU* 3.4 7.2 + - - +
362D SER* 4.6 9.9 - - - -
363D GLY 4.5 2.9 + - - -
364D GLU* 3.6 19.6 + - - +
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Residues in contact with SER 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D LEU 2.9 0.2 + - - -
332D GLU* 1.3 76.7 - - - +
334D MET* 1.3 58.1 + - - +
335D ILE 3.1 2.4 + - - -
336D LYS* 3.3 5.2 + - - +
337D LYS* 3.1 31.6 + - - +
339D ARG 4.1 2.3 + - - -
340D PRO* 3.6 13.9 - - - +
341D THR* 3.7 13.8 + - - -
344D GLU* 2.4 37.9 + - - -
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Residues in contact with MET 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D LEU* 2.8 23.6 + - + +
333D SER* 1.3 73.4 - - - +
335D ILE* 1.3 64.8 + - - +
336D LYS 3.2 1.6 - - - -
337D LYS 3.1 19.0 - - - +
338D PRO 3.3 27.1 - - - +
339D ARG 4.0 0.2 - - - -
340D PRO* 3.7 43.1 - - + -
364D GLU* 4.7 5.5 - - + +
370D TYR* 3.9 20.7 + - + +
373D GLU* 3.6 35.7 - - + +
374D ALA* 3.6 15.9 - - + +
377D MET* 3.9 17.5 - - + -
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Residues in contact with ILE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D LEU 4.3 0.2 + - - -
332D GLU* 3.2 36.8 - - + +
333D SER 3.1 0.6 - - - -
334D MET* 1.3 79.3 - - - +
336D LYS* 1.3 80.4 + - + +
363D GLY* 3.7 32.8 - - - +
364D GLU* 3.9 4.7 - - - +
367D LYS* 4.6 18.8 - - + +
368D GLY* 4.0 17.0 - - - +
369D ASP* 2.9 33.4 + - - +
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Residues in contact with LYS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LYS* 5.5 4.7 + - - -
333D SER 3.3 5.1 + - - +
335D ILE* 1.3 102.0 - - + +
337D LYS* 1.3 64.7 + - + +
338D PRO* 4.4 0.7 - - - +
369D ASP* 3.4 22.0 - - - +
370D TYR* 3.3 16.7 + - - -
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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