Contacts of the helix formed by residues 324 - 328 (chain C) in PDB entry 4GID
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 PRO 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LYS* 6.0 3.4 - - - +
303C GLU* 3.5 24.9 - - - +
318C TRP* 3.3 34.3 - - + +
322C THR 2.9 9.1 - - - +
323C THR* 1.3 81.9 - - + +
325C TRP* 1.3 65.0 + - - +
326C ASN* 3.1 13.2 - - - +
327C ILE* 3.0 39.1 + - + +
328C PHE* 3.5 5.1 - - + -
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Residues in contact with TRP 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C GLY* 5.3 4.0 - - - -
323C THR* 3.0 33.6 + - + -
324C PRO* 1.3 73.1 - - - +
326C ASN* 1.3 62.7 + - - +
328C PHE* 3.0 15.3 + - - +
350C PRO* 3.6 46.4 - - + +
351C GLN* 3.5 43.5 - - + +
354C LEU* 3.9 18.6 - - + -
368C TYR* 3.5 46.4 - + - -
409C VAL* 6.1 0.7 - - + -
411C ASP* 4.0 14.1 - - + +
414C ARG* 2.9 17.7 + - - +
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Residues in contact with ASN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ARG* 4.5 10.9 - - - +
257A ASN 4.9 0.9 - - - +
258A GLY 3.5 19.3 - - - +
259A GLN* 3.4 25.5 + - - +
260A ASP* 2.9 37.7 + - - +
262A LYS* 6.1 2.2 - - - +
257C ASN* 5.8 0.7 + - - -
324C PRO* 3.1 17.0 - - - +
325C TRP* 1.3 79.5 - - - +
327C ILE* 1.3 68.9 + - - +
328C PHE 3.6 4.9 + - - +
411C ASP* 5.8 0.9 - - - -
413C PHE* 6.1 2.2 - - + -
414C ARG* 3.8 11.4 + - - +
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Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLN* 3.3 19.7 - - + +
257C ASN* 5.7 0.9 + - - -
299C ALA* 3.2 23.6 - - - +
300C SER* 3.5 19.8 - - - +
302C THR* 3.9 16.8 - - - +
303C GLU* 4.0 28.5 - - + +
305C PHE* 4.5 0.7 - - + -
324C PRO* 3.0 43.5 + - + +
325C TRP 3.0 0.4 + - - -
326C ASN* 1.3 90.2 - - - +
328C PHE* 1.3 79.2 + - + +
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Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ASN* 4.9 1.5 + - - -
296C ILE* 4.8 5.4 - - + -
300C SER* 4.1 13.2 - - - -
305C PHE* 3.6 35.9 - + - -
309C PHE* 4.8 8.7 - + - -
310C TRP* 4.7 8.7 - + - -
318C TRP* 3.8 26.5 - + - -
323C THR* 5.4 0.9 - - + -
324C PRO* 3.5 17.5 - - + -
325C TRP* 3.0 9.9 + - - +
326C ASN 3.9 0.3 - - - +
327C ILE* 1.3 91.2 - - + +
329C PRO* 1.3 66.2 - - + +
350C PRO* 3.5 16.2 - - + -
353C TYR* 3.4 21.1 - + - +
354C LEU* 3.9 24.5 - - + -
370C PHE* 6.3 0.2 - + - -
414C ARG* 2.9 30.3 + - - -
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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