Contacts of the helix formed by residues 295 - 300 (chain A) in PDB entry 4X2Q
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 PHE 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A HIS* 3.2 42.4 + + + +
292A GLN* 5.2 0.4 - - - -
294A VAL* 1.3 81.8 - - + +
296A PHE* 1.3 64.5 + - - +
297A ASN 3.5 0.2 + - - -
298A GLN* 3.2 16.3 + - - -
299A GLY* 3.4 6.4 + - - +
326A ALA* 5.1 1.6 - - + -
329A ARG* 3.4 44.1 + - - +
341A GLN* 3.8 1.1 - - - -
383A PRO* 3.7 22.4 - - + -
384A THR 3.7 24.2 - - - -
385A VAL* 4.9 4.3 - - + -
403A PRO* 3.3 39.9 - - + -
405A GLN* 3.3 33.4 - - + -
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Residues in contact with PHE 296 (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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112A LYS* 3.3 24.9 - - - -
116A GLN* 3.4 27.6 - - + +
120A VAL* 3.6 32.3 - - + -
121A ASP* 4.9 0.2 - - - -
170A PHE* 3.9 18.6 - + - -
292A GLN* 3.0 40.8 + - - +
293A GLY 5.5 0.4 - - - -
294A VAL 3.3 2.1 - - - +
295A PHE* 1.3 76.4 - - - +
297A ASN* 1.3 69.9 + - + +
299A GLY* 3.3 7.4 + - - -
301A CYS* 3.5 22.8 - - - -
303A THR* 6.1 0.4 - - - -
329A ARG* 4.5 2.7 - - - +
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Residues in contact with ASN 297 (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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112A LYS* 3.2 35.8 - - - +
116A GLN* 4.2 5.8 - - - +
169A ASN* 2.9 28.1 + - - +
170A PHE* 3.4 36.1 - - + -
295A PHE 3.5 0.4 + - - -
296A PHE* 1.3 81.7 - - + +
298A GLN* 1.3 77.5 + - - +
299A GLY 3.1 5.8 + - - -
300A GLN* 3.5 29.9 + - - +
301A CYS* 4.8 0.4 - - + -
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Residues in contact with GLN 298 (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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110A GLY 5.4 1.6 + - - -
111A GLY 4.3 0.4 - - - -
112A LYS* 3.6 20.8 - - - +
113A PRO* 3.2 13.4 - - - +
116A GLN* 4.8 0.9 - - - +
295A PHE 3.2 11.1 + - - -
297A ASN* 1.3 98.8 + - - +
299A GLY* 1.3 54.3 + - - +
300A GLN* 3.3 11.1 + - + +
340A GLU 4.5 1.2 - - - +
341A GLN* 3.9 14.0 - - + -
342A GLY* 3.0 40.9 + - - +
343A PRO 3.4 24.1 + - - +
344A GLN* 3.3 28.0 + - - +
403A PRO* 3.3 18.6 - - - +
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Residues in contact with GLY 299 (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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294A VAL 3.2 23.5 - - - +
295A PHE* 3.4 4.7 + - - -
296A PHE 3.3 6.7 + - - -
297A ASN 3.1 3.0 + - - -
298A GLN* 1.3 75.2 - - - +
300A GLN* 1.3 57.9 + - - +
301A CYS* 2.8 18.5 + - - +
304A ALA* 5.5 0.5 - - - +
400A ILE 5.0 1.6 - - - +
401A PHE* 4.2 3.6 - - - -
402A GLY 3.4 24.5 + - - +
403A PRO 4.2 0.2 - - - -
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Residues in contact with GLN 300 (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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110A GLY 5.3 3.4 + - - -
168A TRP* 3.4 31.8 - - + -
169A ASN* 3.0 15.7 - - - +
297A ASN* 3.5 27.4 + - - +
298A GLN* 3.3 9.0 + - - +
299A GLY* 1.3 69.9 - - - +
301A CYS* 1.3 60.0 + - - +
343A PRO 4.5 3.8 + - - -
344A GLN* 3.0 28.9 + - - +
345A ILE* 3.3 26.4 - - - +
349A GLN* 3.1 23.8 + - - +
401A PHE* 3.4 23.1 + - + +
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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