Contacts of the strand formed by residues 387 - 392 (chain C) in PDB entry 1G88
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 VAL 387 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C THR* 3.6 7.8 - - - +
350C VAL* 3.1 37.5 + - + +
385C LYS 4.1 2.0 - - - +
386C GLY* 1.3 79.1 - - - +
388C GLN* 1.3 62.3 + - - +
389C LEU* 3.8 27.4 - - + -
399C VAL* 4.3 7.0 - - + -
400C ARG 3.4 9.9 - - - +
401C CYS* 4.2 9.4 - - - -
402C LEU* 4.3 2.7 - - - +
407C VAL* 3.9 33.2 - - + -
503C MET* 3.9 22.0 - - + -
505C PHE* 4.0 9.8 - - + -
525C ILE* 5.4 0.4 - - + -
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Residues in contact with GLN 388 (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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347C ILE* 3.2 45.1 - - + +
348C VAL 3.5 5.2 - - - +
349C THR* 4.1 11.3 + - - +
387C VAL* 1.3 75.4 - - - +
389C LEU* 1.3 64.9 + - - +
390C GLU* 3.9 4.7 + - + +
398C TRP 3.6 0.5 - - - +
399C VAL* 3.3 6.1 - - - -
400C ARG* 3.0 57.2 + - + +
402C LEU* 3.2 27.4 - - + +
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Residues in contact with LEU 389 (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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323C TRP* 3.4 18.2 - - + -
324C CYS* 5.5 0.2 - - - -
326C ILE* 4.2 19.7 - - + -
347C ILE* 4.4 1.3 - - - -
348C VAL* 3.0 40.7 + - + +
350C VAL* 4.6 4.7 - - + -
387C VAL* 3.8 19.3 - - + -
388C GLN* 1.3 75.5 - - - +
390C GLU* 1.3 60.8 + - - +
397C VAL* 4.9 6.3 - - + -
398C TRP 3.3 4.0 - - - +
399C VAL* 3.7 27.6 - - + -
501C LEU* 6.3 0.4 - - + -
503C MET* 3.9 7.4 - - + -
525C ILE* 4.5 6.5 - - + -
527C ILE* 3.4 37.2 - - + -
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Residues in contact with GLU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TRP* 4.1 2.0 - - - -
346C PRO* 3.4 4.7 - - + +
347C ILE* 3.4 34.5 - - + +
388C GLN* 3.9 5.1 + - + +
389C LEU* 1.3 74.2 - - - +
391C CYS* 1.3 65.5 + - - +
392C LYS* 3.0 29.0 + - + +
396C ASP 3.6 0.3 - - - +
397C VAL* 3.4 7.3 - - - +
398C TRP* 2.8 42.3 + - + +
400C ARG* 4.4 5.5 + - - -
434C TYR* 2.8 28.8 + - + -
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Residues in contact with CYS 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TRP* 3.6 45.1 - - + +
346C PRO* 2.8 33.9 + - + +
390C GLU* 1.3 75.9 - - - +
392C LYS* 1.3 63.4 + - - +
393C GLY 4.2 14.4 + - - +
394C GLU 4.9 2.2 - - - -
395C GLY* 4.4 14.6 - - - -
396C ASP 3.3 8.3 - - - -
397C VAL* 5.5 0.7 - - - -
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Residues in contact with LYS 392 (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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390C GLU* 3.0 23.6 - - + +
391C CYS* 1.3 72.6 - - - +
393C GLY* 1.3 64.3 + - - +
395C GLY* 4.3 0.2 - - - -
396C ASP* 2.9 43.5 + - + +
398C TRP* 3.2 47.3 - - + +
434C TYR* 2.7 41.1 + - - -
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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