Contacts of the helix formed by residues 321 - 329 (chain A) in PDB entry 2FGY
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 ASN 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ILE 2.9 25.0 + - - +
319A VAL 3.8 2.0 + - - -
320A ASP* 1.3 72.5 + - - +
322A THR* 1.3 53.8 + - - +
323A VAL 3.3 0.2 - - - -
324A THR* 3.5 17.5 - - - +
325A TYR* 2.8 32.9 + - - +
372A LEU* 3.0 48.2 + - + +
375A ASN* 2.9 32.1 + - - +
376A LEU* 3.5 18.9 - - - +
379A ILE* 4.0 4.6 - - + +
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Residues in contact with THR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 2.9 53.8 - - + +
40A ALA* 3.7 13.6 - - - +
296A ASP* 5.8 0.2 + - - -
299A THR* 4.8 1.0 + - - -
301A ALA* 3.3 23.6 - - - +
302A ILE 4.5 0.6 + - - -
320A ASP* 3.1 15.2 + - - +
321A ASN* 1.3 78.1 - - - +
323A VAL* 1.3 66.2 + - + +
325A TYR* 3.6 3.3 + - - +
326A ALA* 3.3 21.5 + - - +
379A ILE* 4.4 2.4 - - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO 5.6 0.2 - - - -
319A VAL* 5.6 1.6 - - + -
320A ASP* 3.1 39.7 + - + +
322A THR* 1.3 79.2 - - + +
324A THR* 1.3 66.3 + - - +
326A ALA* 3.4 5.9 + - - +
327A GLN* 2.9 45.6 + - + +
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL* 3.4 20.7 - - + +
320A ASP 3.1 13.4 + - - -
321A ASN* 3.5 18.6 + - - +
323A VAL* 1.3 79.8 - - - +
325A TYR* 1.3 58.4 + - - +
327A GLN* 3.4 6.5 + - - -
328A THR* 2.7 40.7 + - + +
339A ILE* 5.1 3.8 - - + -
340A ILE* 3.4 43.7 - - + +
343A ALA* 5.2 4.1 - - + +
372A LEU* 5.8 0.2 - - + -
376A LEU* 4.6 1.6 - - + -
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Residues in contact with TYR 325 (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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40A ALA* 3.4 35.9 - - + -
41A CYS* 4.6 2.6 - - + +
49A CYS* 3.3 24.5 + - + +
51A HIS* 3.5 30.6 + + + -
321A ASN 2.8 17.7 + - - +
322A THR 3.7 5.8 - - - +
323A VAL 3.3 0.2 - - - -
324A THR* 1.3 78.0 - - - +
326A ALA* 1.3 56.9 + - - +
328A THR* 3.5 2.8 + - - -
329A LEU* 3.0 42.8 + - + +
376A LEU* 3.8 27.6 - - + +
379A ILE* 3.7 26.5 - - + -
380A ASP* 2.4 34.0 + - - -
383A VAL* 5.3 1.7 - - + +
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Residues in contact with ALA 326 (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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39A PRO 4.9 2.9 - - - +
40A ALA* 3.7 19.5 - - - +
42A ILE* 3.9 25.1 - - + +
322A THR 3.3 14.7 + - - +
323A VAL* 3.9 5.4 - - - +
324A THR 3.3 0.2 - - - -
325A TYR* 1.3 81.0 - - - +
327A GLN* 1.3 62.9 + - + +
328A THR 3.4 0.7 + - - -
329A LEU* 3.7 13.8 + - - +
330A HIS* 5.0 6.6 - - - -
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Residues in contact with GLN 327 (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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323A VAL* 2.9 34.0 + - + +
324A THR* 4.0 6.4 - - - +
325A TYR 3.3 0.4 - - - -
326A ALA* 1.3 79.2 - - + +
328A THR* 1.3 60.3 + - + +
329A LEU 3.6 0.2 - - - -
330A HIS 5.3 0.6 + - - -
331A LEU* 3.9 15.9 - - - +
339A ILE* 4.7 15.7 - - + +
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Residues in contact with THR 328 (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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51A HIS* 2.6 33.8 + - - -
52A PRO* 3.9 4.2 - - - +
324A THR* 2.7 29.2 + - + +
325A TYR* 4.0 0.2 - - - -
327A GLN* 1.3 76.0 - - - +
329A LEU* 1.3 66.4 + - - +
330A HIS 3.2 3.1 - - - -
331A LEU* 3.1 22.5 + - + +
336A ALA* 3.7 27.3 - - + +
339A ILE* 3.6 37.2 - - + -
340A ILE* 4.5 0.9 - - + -
376A LEU* 4.8 2.1 - - - +
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Residues in contact with LEU 329 (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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40A ALA 5.1 2.7 - - - +
42A ILE* 5.9 6.1 - - + +
43A THR* 6.4 1.6 - - + -
49A CYS* 3.5 42.6 - - + -
50A ARG 3.7 24.9 - - - +
51A HIS* 3.9 10.5 - - + -
52A PRO* 3.4 17.8 - - - +
325A TYR* 3.0 34.5 + - + +
326A ALA* 3.7 10.7 + - - +
327A GLN 3.6 1.2 - - - -
328A THR* 1.3 77.0 - - - +
330A HIS* 1.3 86.5 + - + +
331A LEU 4.4 0.2 - - - +
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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