Contacts of the strand formed by residues 350 - 353 (chain M) 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 350 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349L GLU* 3.0 33.7 + - - -
352L MET* 4.1 22.5 - - - +
356L ARG* 3.9 13.3 - - - +
373L LYS* 5.2 0.9 - - - +
197M GLU* 2.3 56.1 + - - +
200M GLU* 5.1 2.2 - - - +
201M ALA* 4.5 7.5 - - + +
220M PRO* 4.1 13.2 - - + -
222M GLY 3.8 1.6 + - - -
223M VAL* 3.1 26.1 - - + +
224M LEU* 3.0 25.8 + - - +
348M LEU 4.9 0.4 - - - -
349M ASP* 1.3 99.9 - - + +
351M LYS* 1.3 61.8 + - - +
352M ILE* 3.8 12.0 - - + +
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Residues in contact with LYS 351 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377L SER* 3.9 28.4 + - - +
380L LEU* 3.6 32.7 - - + +
381L GLU* 3.3 17.8 + - - +
224M LEU* 4.1 17.9 - - + -
226M TYR* 4.1 4.6 + - + +
343M LEU* 3.1 57.9 + - - +
344M ARG 3.4 7.7 + - - -
345M SER* 4.2 1.0 - - - +
348M LEU 3.9 10.8 - - - +
349M ASP 3.9 5.7 + - - +
350M ARG* 1.3 75.4 - - - +
352M ILE* 1.3 67.3 + - - +
353M GLU 4.1 1.0 + - - -
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Residues in contact with ILE 352 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M GLN* 3.3 37.7 - - + +
197M GLU* 2.8 40.4 - - + +
198M LEU* 5.9 2.0 - - + +
223M VAL* 3.2 29.4 - - + -
224M LEU 3.1 12.0 + - - +
225M MET* 3.7 6.2 - - + +
226M TYR* 3.1 29.2 + - - -
350M ARG* 3.5 15.3 - - + +
351M LYS* 1.3 85.3 - - - +
353M GLU* 1.3 62.2 + - - +
354M PHE* 3.9 11.4 - - + -
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Residues in contact with GLU 353 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M LYS* 4.2 16.5 + - - +
194M GLN* 3.1 24.3 + - + +
226M TYR* 3.3 31.8 + - + +
227M GLY* 6.0 0.2 - - - -
351M LYS 4.1 1.2 + - - -
352M ILE* 1.3 72.5 - - - +
354M PHE* 1.3 73.7 + - - +
355M PRO* 3.9 22.5 - - + +
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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