Contacts of the strand formed by residues 323 - 330 (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 PHE 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C ASN* 5.5 0.2 - - - -
281C MET* 5.4 4.5 - - + -
283C LEU* 6.4 0.2 - - + -
320C MET* 5.4 5.8 - - + -
321C PRO* 3.7 20.4 - - + -
322C ARG* 1.3 75.1 - - - +
324C ARG* 1.3 71.6 + - - +
325C ILE* 3.6 23.1 - - + -
373C LEU* 3.6 27.8 - - + -
374C GLU* 3.6 1.0 - - - -
375C VAL* 2.9 67.6 + - + +
408C PHE* 4.4 8.3 - + - -
410C VAL* 4.6 7.0 - - + -
426C VAL* 3.5 33.4 - - + -
429C PRO* 4.7 22.2 - - + +
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Residues in contact with ARG 324 (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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75C ASN* 5.0 4.2 + - - -
323C PHE* 1.3 81.6 - - - +
325C ILE* 1.3 73.5 + - - +
372C PHE* 4.6 11.2 - - + -
373C LEU 3.2 9.0 - - - +
374C GLU* 3.6 28.7 - - - +
428C ASN 5.5 0.7 - - - +
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Residues in contact with ILE 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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75C ASN* 3.6 27.1 - - + +
76C ILE 3.8 10.8 - - - +
77C PHE* 3.3 26.5 - - + -
323C PHE* 3.6 28.5 - - + -
324C ARG* 1.3 86.4 - - - +
326C GLU* 1.3 62.4 + - - +
327C ASP* 4.2 9.4 - - - +
371C ALA 3.7 0.7 - - - +
372C PHE* 3.0 6.3 - - - -
373C LEU* 2.8 45.1 + - + +
410C VAL* 6.0 0.7 - - + -
425C ARG 3.5 25.4 - - - +
426C VAL* 4.5 0.4 - - + -
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Residues in contact with GLU 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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197C ARG 5.5 1.9 - - - +
199C THR* 5.1 6.3 - - - +
325C ILE* 1.3 74.0 - - - +
327C ASP* 1.3 63.0 + - - +
370C LYS* 3.3 29.0 + - - +
371C ALA 3.3 5.6 - - - +
372C PHE* 2.9 36.0 - - + -
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Residues in contact with ASP 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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70C LYS* 2.6 37.0 + - - -
75C ASN 3.5 11.1 - - - +
76C ILE* 3.5 0.3 - - - -
77C PHE* 3.1 33.4 + - + +
325C ILE* 4.1 3.2 - - - +
326C GLU* 1.3 74.7 - - - +
328C GLY* 1.3 64.6 + - - +
329C PHE* 3.5 17.3 - - + -
369C HIS 3.6 0.5 - - - +
370C LYS* 2.9 13.6 - - - +
371C ALA 2.6 40.2 + - - +
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Residues in contact with GLY 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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201C VAL 5.0 6.7 - - - -
326C GLU 4.3 0.6 + - - -
327C ASP* 1.3 78.9 + - - +
329C PHE* 1.3 66.5 - - - +
369C HIS 3.4 6.3 - - - -
370C LYS* 3.5 19.5 - - - +
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Residues in contact with PHE 329 (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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62C PHE* 4.7 2.7 - + - -
66C LEU* 3.3 47.6 - - + -
70C LYS* 4.3 8.1 - - - -
77C PHE 3.9 10.1 - - - -
78C LEU* 4.0 2.5 - - + -
201C VAL 5.4 2.2 + - - -
327C ASP* 3.5 31.4 - - + -
328C GLY* 1.3 86.0 - - - +
330C SER* 1.3 68.4 + - - +
331C LEU* 3.5 23.5 + - + -
334C GLN* 5.5 2.2 - - + +
367C ALA 3.4 1.2 - - - +
368C PHE* 3.7 8.7 - - - -
369C HIS* 3.2 55.8 + + - +
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Residues in contact with SER 330 (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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329C PHE* 1.3 74.0 - - - +
331C LEU* 1.3 62.9 + - - +
332C LYS* 3.1 12.8 + - - +
333C GLU* 3.9 6.2 + - - +
334C GLN* 3.6 21.3 + - - +
366C ASP* 2.5 30.4 + - - -
367C ALA 3.2 7.0 - - - -
368C PHE* 4.4 14.9 - - - -
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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