Contacts of the strand formed by residues 320 - 324 (chain A) in PDB entry 5GJE
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 LEU 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A LEU 3.5 5.8 - - - +
315A ALA* 4.1 15.7 - - + -
319A ASP* 1.3 82.8 - - - +
321A ARG* 1.3 64.6 + - - +
335A LEU* 2.8 26.6 - - - +
336A GLN 3.5 8.0 + - - +
337A LEU* 4.8 14.1 - - + -
340A ILE* 4.0 19.5 - - + +
343A ALA* 4.3 15.9 - - + -
346A ILE* 3.7 22.4 - - + -
355A ILE* 3.9 13.7 - - + -
357A TRP* 3.6 37.7 - - + -
368A SER* 6.1 0.2 - - - +
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Residues in contact with ARG 321 (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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313A LEU* 3.4 3.9 - - - +
314A LEU* 2.5 52.6 + - + +
316A ARG* 2.8 40.1 - - + +
319A ASP* 3.0 22.6 + - - +
320A LEU* 1.3 83.2 - - - +
322A ARG* 1.3 57.9 + - - +
333A ILE* 4.0 34.2 - - + +
334A VAL* 3.1 11.1 - - - +
335A LEU* 3.2 41.6 - - + +
346A ILE* 5.6 0.2 - - - +
553A LEU* 4.3 12.9 - - - +
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Residues in contact with ARG 322 (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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311A LEU* 4.1 26.8 - - + +
312A LEU 3.4 4.7 - - - +
313A LEU* 3.8 21.3 - - + +
321A ARG* 1.3 74.6 - - - +
323A ILE* 1.3 61.7 + - - +
324A SER 4.2 0.5 + - - -
332A ASP 3.8 1.4 - - - +
333A ILE* 3.7 1.6 - - - -
334A VAL* 2.8 59.7 + - + +
335A LEU 5.2 0.6 - - - -
370A ILE* 3.0 35.1 - - + +
371A ASP* 2.7 38.1 + - - +
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Residues in contact with ILE 323 (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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311A LEU* 3.5 2.8 - - - -
312A LEU* 2.5 53.3 + - + +
314A LEU* 4.3 16.4 - - + +
321A ARG 4.3 0.2 - - - -
322A ARG* 1.3 73.5 - - - +
324A SER* 1.3 73.7 + - - +
325A LEU* 5.3 0.4 - - + -
330A PHE* 3.1 36.6 - - + +
332A ASP 3.8 3.6 - - - +
333A ILE* 3.5 35.2 - - + -
536A ILE* 4.5 3.1 - - + -
549A ILE* 4.6 8.7 - - + -
550A ILE* 3.8 29.8 - - + -
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Residues in contact with SER 324 (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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293A THR 5.2 0.2 - - - -
294A GLY* 3.1 39.5 + - - -
308A ALA* 3.7 10.6 - - - +
311A LEU* 3.8 13.3 - - - +
322A ARG 4.1 1.4 + - - -
323A ILE* 1.3 91.1 - - - +
325A LEU* 1.3 65.3 + - - +
326A ASP* 2.9 14.2 + - - +
327A THR* 3.9 7.7 + - - +
329A ASP* 5.9 0.9 - - - -
330A PHE* 4.1 8.5 - - - -
332A ASP 4.5 3.2 + - - -
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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