Contacts of the strand formed by residues 355 - 358 (chain A) in PDB entry 3GG0
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 THR 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASP 2.9 14.3 + - - -
321A LYS* 3.6 28.4 - - + +
322A ILE 2.7 32.6 + - - +
354A ILE* 1.3 73.4 - - - +
356A VAL* 1.3 60.5 + - - +
357A VAL 4.2 0.2 - - - -
377A LEU* 3.4 32.3 - - + -
121B VAL 4.6 1.2 + - - -
122B ASN* 5.0 5.2 + - - +
127B ARG* 2.9 33.3 + - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.4 5.2 - - + +
324A VAL* 3.9 26.5 - - + -
345A VAL* 4.5 10.5 - - + -
346A VAL* 4.4 17.5 - - + +
349A CYS* 3.4 35.0 - - + -
350A GLU 5.3 0.2 - - - +
354A ILE 3.5 2.9 + - - +
355A THR* 1.3 75.5 - - - +
357A VAL* 1.3 64.3 + - - +
375A ILE* 4.3 25.1 - - + +
376A ARG 4.9 1.0 + - - -
377A LEU* 3.4 24.9 + - - +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 4.0 22.0 - - + -
321A LYS* 3.7 28.9 - - + -
322A ILE 2.9 8.4 + - - +
323A LYS* 3.4 13.0 - - + -
324A VAL* 2.7 34.7 + - - +
356A VAL* 1.3 79.0 - - - +
358A ALA* 1.3 71.5 + - - +
359A GLU* 5.1 0.9 - - + -
377A LEU* 3.3 27.1 - - + +
379A GLN* 4.0 22.4 - - + +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A VAL* 4.2 6.7 - - + -
329A VAL* 4.1 5.6 - - + -
357A VAL* 1.3 75.4 - - - +
359A GLU* 1.3 59.8 + - - +
361A VAL* 3.8 2.6 - - + +
370A LEU* 3.8 31.4 - - + -
375A ILE* 3.9 26.5 - - + +
377A LEU 3.0 7.9 + - - -
378A PHE* 3.7 6.6 - - + -
379A GLN 2.9 28.2 + - - +
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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
------------------------------------------------------------
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