Contacts of the strand formed by residues 366 - 375 (chain C) in PDB entry 2GD4
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 ASP 366 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C ALA* 4.6 10.4 - - - +
213C LEU 3.8 1.4 + - - -
214C VAL* 3.1 13.5 - - + +
215C LEU 2.8 29.3 + - - -
330C SER* 2.5 29.8 + - - -
332C LYS* 2.8 29.9 + - - +
364C VAL* 3.4 8.8 - - - +
365C SER* 1.3 87.8 - - - +
367C ALA* 1.3 53.8 + - - +
368C PHE* 3.8 29.8 - - + -
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 3.8 14.4 - - + -
215C LEU* 3.2 23.6 - - + -
329C PHE 3.4 0.3 - - - +
330C SER* 3.2 7.4 - - - -
331C LEU* 2.8 55.5 + - + +
332C LYS* 4.4 7.7 - - + +
344C PHE* 5.4 0.4 - - + -
364C VAL* 5.2 1.6 - - + -
366C ASP* 1.3 78.9 + - - +
368C PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C VAL* 4.0 16.1 - - + +
202C ILE* 3.4 37.2 - - + -
203C PRO* 3.5 28.0 - - + -
206C ALA* 3.4 28.3 - - + -
207C ILE* 4.8 2.2 - - + -
214C VAL* 4.5 12.1 - - + -
215C LEU 2.5 14.5 + - - +
216C VAL* 3.4 7.4 - - + +
217C ASN* 3.1 26.8 + - - +
329C PHE* 3.7 11.2 - - - -
330C SER* 4.4 15.3 - - - -
331C LEU* 4.8 0.7 - - - -
366C ASP* 3.8 31.2 - - + -
367C ALA* 1.3 75.2 - - - +
369C HIS* 1.3 60.5 + - - +
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Residues in contact with HIS 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.5 7.2 - - + +
79C SER* 3.1 36.8 + - - -
82C SER* 4.1 12.1 - - - -
83C ILE* 3.3 29.7 - - + +
201C VAL* 5.0 0.8 - - - +
217C ASN* 2.9 33.9 + - - +
219C ILE* 5.2 3.6 - - + -
327C ASP 3.6 0.9 - - - +
328C GLY* 3.4 2.8 - - - -
329C PHE* 3.2 53.0 + + + +
331C LEU* 3.6 21.3 - - + -
367C ALA 3.9 0.4 + - - -
368C PHE* 1.3 73.6 - - - +
370C LYS* 1.3 62.8 + - - +
371C ALA* 4.1 9.2 - - + +
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Residues in contact with LYS 370 (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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198C ILE* 3.5 25.7 - - + +
199C THR 3.7 21.7 + - - +
200C ASP* 4.9 5.7 + - - +
201C VAL* 4.0 18.6 - - + +
217C ASN 3.1 8.3 + - - -
218C THR* 3.0 23.0 - - + +
219C ILE 2.9 23.4 + - - +
326C GLU* 3.3 40.1 + - - +
327C ASP 2.9 24.2 - - - +
328C GLY* 3.5 17.8 - - - +
369C HIS* 1.3 73.7 - - - +
371C ALA* 1.3 60.3 + - - +
372C PHE* 6.1 0.2 - - - -
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Residues in contact with ALA 371 (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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77C PHE* 3.6 19.0 - - + +
78C LEU* 3.6 33.2 - - - +
79C SER 4.6 0.4 - - - +
219C ILE* 3.3 11.4 - - + +
325C ILE 3.7 0.3 - - - +
326C GLU* 3.3 2.3 - - - +
327C ASP* 2.6 38.3 + - + +
369C HIS* 4.1 10.4 - - + +
370C LYS* 1.3 75.9 - - - +
372C PHE* 1.3 61.4 + - - +
422C PHE* 5.6 0.2 - - + -
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Residues in contact with PHE 372 (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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77C PHE* 3.6 6.5 - - - -
197C ARG* 5.0 12.6 - - + -
198C ILE* 3.8 21.5 - - + -
219C ILE 2.9 8.5 + - - +
220C TYR* 3.1 41.2 - + - -
221C PHE 3.1 24.8 + - - -
324C ARG* 4.6 9.0 - - + -
325C ILE 3.0 14.6 - - - -
326C GLU* 2.9 46.9 - - + -
370C LYS* 5.9 0.9 - - + -
371C ALA* 1.3 75.9 - - - +
373C LEU* 1.3 66.3 + - - +
374C GLU* 4.2 19.1 - - - -
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Residues in contact with LEU 373 (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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77C PHE* 3.3 47.1 - - + -
221C PHE* 3.6 25.1 - - + +
281C MET* 5.2 3.4 - - + -
323C PHE* 3.6 30.7 - - + -
324C ARG* 3.2 8.0 - - - +
325C ILE* 2.8 37.5 + - + +
372C PHE* 1.3 78.2 - - - +
374C GLU* 1.3 74.8 + - - +
375C VAL* 4.0 10.5 - - + -
410C VAL* 4.6 13.0 - - + -
412C ILE* 4.3 7.6 - - + -
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Residues in contact with GLU 374 (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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220C TYR* 3.7 20.4 + - + +
221C PHE 3.1 8.9 + - - +
222C LYS* 3.0 53.3 + - + +
223C GLY 4.5 2.9 + - - -
323C PHE 3.8 1.7 - - - +
324C ARG* 3.6 24.1 - - - +
372C PHE* 4.2 12.6 - - + -
373C LEU* 1.3 78.5 - - - +
375C VAL* 1.3 76.6 + - - +
376C ASN* 4.6 13.0 - - - +
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Residues in contact with VAL 375 (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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222C LYS* 5.6 0.4 - - - -
225C TRP* 4.1 25.1 - - + -
252C MET* 4.7 4.0 - - + -
281C MET* 4.2 14.1 - - + -
320C MET* 4.8 2.7 - - - -
321C PRO 4.2 8.3 - - - +
322C ARG* 3.2 7.1 - - - +
323C PHE* 2.9 72.6 + - + +
373C LEU* 4.0 12.6 - - + -
374C GLU* 1.3 91.1 - - - +
376C ASN* 1.3 61.2 + - - +
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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