Contacts of the strand formed by residues 408 - 414 (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 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C PHE* 4.3 2.2 - + - -
283C LEU* 4.4 20.9 - - + -
284C ILE 3.5 13.7 - - - +
285C LEU* 4.1 13.9 - - + -
292C LEU* 3.7 6.4 - - - +
320C MET* 5.1 4.0 - - + -
321C PRO* 4.0 20.2 - - + -
323C PHE* 4.4 7.2 - + - -
404C ALA* 3.6 29.4 - - + -
406C ARG 3.3 20.6 - - - +
407C PRO* 1.3 75.0 - - - +
409C LEU* 1.3 69.8 + - - +
410C VAL* 3.9 7.9 - - + -
425C ARG* 3.8 0.7 - - - +
426C VAL* 2.9 76.0 + - + +
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Residues in contact with LEU 409 (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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63C TYR* 3.4 31.9 - - + +
283C LEU* 3.6 3.3 - - - -
284C ILE* 3.0 39.6 + - + +
292C LEU* 3.7 20.2 - - + -
295C VAL* 3.7 24.9 - - + -
296C GLU* 4.1 9.0 - - + -
299C LEU* 4.8 6.7 - - + -
307C TRP* 4.1 19.3 - - + -
408C PHE* 1.3 87.0 - - - +
410C VAL* 1.3 65.0 - - - +
411C PHE* 4.5 9.9 - - + -
424C GLY 3.6 3.8 - - - +
425C ARG* 4.1 11.0 - - + +
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PHE* 5.1 2.7 - - + -
281C MET* 4.1 24.7 - - + -
282C VAL 4.1 2.7 - - - -
283C LEU* 4.8 2.7 - - + +
323C PHE* 4.6 6.5 - - + -
325C ILE* 6.0 0.4 - - + -
373C LEU* 4.6 18.4 - - + -
408C PHE* 3.9 5.4 - - + -
409C LEU* 1.3 82.6 - - - +
411C PHE* 1.3 79.9 + - - +
412C ILE* 4.6 5.8 - - + -
423C MET* 4.5 1.0 - - - +
424C GLY* 2.5 48.9 + - - +
425C ARG 4.2 0.7 - - - +
426C VAL* 3.6 31.2 - - + +
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Residues in contact with PHE 411 (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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281C MET* 3.0 29.3 - - - +
282C VAL* 3.0 32.5 + - + -
284C ILE* 3.6 34.3 - - + -
299C LEU* 4.7 6.7 - - + -
304C LEU* 3.1 35.9 - - + -
307C TRP* 3.6 10.3 - + - -
308C LEU* 6.6 0.2 - - + -
409C LEU* 4.5 10.5 - - + -
410C VAL* 1.3 86.4 - - - +
412C ILE* 1.3 62.9 + - - +
413C ARG* 4.1 3.1 - - + -
420C ILE* 4.1 21.3 - - + -
422C PHE 3.5 4.5 - - - -
423C MET* 3.4 34.5 - - + -
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Residues in contact with ILE 412 (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* 4.8 2.7 - - + -
221C PHE* 4.0 25.6 - - + -
274C PHE* 4.5 6.1 - - + -
279C ILE* 4.0 22.4 - - + -
280C THR 3.6 3.4 - - - +
281C MET* 3.9 19.5 - - + -
373C LEU* 4.3 14.6 - - + -
410C VAL* 4.6 5.4 - - + -
411C PHE* 1.3 79.6 - - - +
413C ARG* 1.3 54.8 + - - +
420C ILE* 3.4 2.5 - - - +
421C ILE* 2.7 37.1 + - + +
422C PHE* 2.7 62.6 + - + -
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Residues in contact with ARG 413 (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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259C ARG* 4.6 4.6 - - - +
271C GLU* 2.3 33.2 + - - +
279C ILE* 3.4 12.3 - - - +
280C THR* 3.1 44.4 + - - +
282C VAL* 4.6 12.3 - - + +
308C LEU* 2.8 47.1 - - - +
311C LEU* 4.3 11.1 - - - +
411C PHE* 5.9 1.8 - - + -
412C ILE* 1.3 75.8 - - - +
414C GLU* 1.3 66.3 + - - +
415C VAL* 5.1 8.6 - - - +
418C ASN* 3.3 24.0 + - - +
419C THR 2.9 18.4 - - - +
420C ILE* 4.3 6.3 - - + -
421C ILE* 4.1 6.3 - - - +
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Residues in contact with GLU 414 (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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129C ARG* 2.7 40.0 + - - -
130C LEU* 3.3 29.8 - - + -
133C LYS* 3.1 9.7 + - + +
278C ASP 3.6 10.8 - - - +
279C ILE* 4.2 7.4 - - + -
413C ARG* 1.3 81.7 - - - +
415C VAL* 1.3 59.2 + - - +
416C PRO* 2.7 22.0 - - + +
417C LEU* 2.3 37.4 + - - +
418C ASN* 2.9 25.6 - - - -
419C THR* 2.9 15.6 + - - +
421C ILE* 4.4 0.6 - - + +
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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