Contacts of the strand formed by residues 297 - 300 (chain L) in PDB entry 5GJQ
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 ARG 297 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381K GLU* 2.2 48.6 + - + +
384K MET* 4.6 8.9 - - - +
388K ARG* 5.9 1.6 - - - +
405K THR* 3.9 39.6 + - + +
408K LYS* 5.7 2.7 - - - +
144L GLU* 3.0 56.2 + - - +
148L VAL* 4.1 18.8 - - - +
169L GLY 3.6 2.0 + - - +
170L CYS* 3.7 29.2 - - - -
171L LEU 3.9 0.8 + - - -
295L LEU* 5.3 1.8 - - - -
296L ASP* 1.3 82.7 - - - +
298L LYS* 1.3 77.1 + - + +
299L ILE* 3.7 7.0 + - - +
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Residues in contact with LYS 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406K VAL* 4.8 3.4 + - - +
408K LYS* 4.2 40.4 + - + +
409K LYS* 5.7 4.2 - - - +
144L GLU* 4.8 2.1 - - - +
171L LEU* 3.7 20.4 - - + +
173L TYR* 3.4 27.0 - - + +
290L LEU* 4.1 34.4 + - + +
292L PRO* 5.4 6.3 - - - +
295L LEU* 5.0 4.9 - - + -
296L ASP 4.6 11.7 + - - -
297L ARG* 1.3 88.1 + - - +
299L ILE* 1.3 61.2 + - - +
300L HIS 3.9 2.2 + - - -
388L PRO* 4.4 16.4 + - + +
389L VAL* 5.5 7.2 - - - +
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Residues in contact with ILE 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L GLN* 3.2 37.7 - - + -
144L GLU* 4.6 17.5 - - + +
145L LEU* 2.8 50.9 - - + +
148L VAL* 5.0 1.1 - - + -
170L CYS* 3.6 18.2 - - + -
171L LEU 3.0 9.4 + - - +
172L LEU* 3.2 41.3 - - + +
173L TYR* 3.3 7.6 + - - -
297L ARG* 3.7 8.5 + - - +
298L LYS* 1.3 75.6 - - - +
300L HIS* 1.3 58.6 + - - +
301L ILE* 3.9 0.4 + - + -
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Residues in contact with HIS 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L GLN* 2.4 32.1 + - - +
173L TYR* 2.8 59.4 + + - +
174L GLY* 4.5 8.3 - - - -
175L PRO* 4.6 4.7 - - + +
298L LYS 3.9 3.4 + - - -
299L ILE* 1.3 72.7 - - - +
301L ILE* 1.3 55.1 + - - +
302L ASP* 2.7 41.0 + - + -
386L TYR 5.6 3.8 - - - -
387L LYS* 5.6 4.0 - - + -
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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