Contacts of the strand formed by residues 46 - 50 (chain C) in PDB entry 4QGC
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 GLY 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.9 0.2 - - - -
44C ASN 3.8 2.6 + - - -
45C THR* 1.3 75.0 + - - +
47C ILE* 1.3 63.8 + - - +
48C ILE* 5.1 0.2 - - - -
70C ASN* 3.4 10.8 - - - -
71C VAL* 6.5 0.2 - - - -
357C ASP 3.0 11.5 + - - -
358C CYS* 3.3 19.0 - - - +
359C ILE* 2.9 26.7 + - - +
464C HIS 4.1 8.7 + - - -
467C ARG* 5.6 0.2 - - - +
1004C GOL 4.2 6.8 - - - -
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Residues in contact with ILE 47 (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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43C ARG* 3.4 35.0 - - - +
45C THR* 4.3 1.6 - - - +
46C GLY* 1.3 74.9 - - - +
48C ILE* 1.3 64.5 + - - +
49C CYS* 3.7 23.2 + - - -
68C GLY 3.7 17.5 - - - +
69C MET* 4.1 1.9 - - - -
70C ASN* 2.8 35.6 + - - +
71C VAL 3.2 7.1 + - - +
359C ILE 3.6 3.1 - - - +
361C LEU* 4.9 2.7 - - + -
375C VAL* 4.1 9.0 - - + +
378C GLN* 3.8 26.9 - - + +
379C HIS* 3.7 30.5 - - + +
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 1.3 74.6 - - - +
49C CYS* 1.3 63.3 + - - +
71C VAL* 3.5 35.2 - - + +
73C ARG* 4.0 17.3 - - + -
241C PHE* 4.1 13.0 - - + -
325C ILE* 3.6 38.6 - - + -
358C CYS* 3.9 23.6 - - + -
359C ILE 2.9 13.2 + - - +
360C MET* 3.3 19.4 - - + +
361C LEU* 2.8 30.7 + - - +
465C LEU* 4.8 4.3 - - + -
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Residues in contact with CYS 49 (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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47C ILE* 3.7 16.8 - - - -
48C ILE* 1.3 78.3 - - - +
50C THR* 1.3 57.8 + - - +
51C ILE* 3.5 2.2 + - + +
64C MET* 3.7 19.7 - - + -
69C MET* 3.6 26.9 - - - -
71C VAL 2.9 9.1 + - - -
72C ALA* 3.5 5.5 - - - -
73C ARG* 2.7 30.9 + - - -
361C LEU* 4.0 4.7 - - - -
365C THR* 3.9 10.3 - - - +
375C VAL* 3.7 28.9 - - - -
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Residues in contact with THR 50 (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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49C CYS* 1.3 70.8 - - - +
51C ILE* 1.3 64.8 + - - +
55C SER* 3.7 0.5 + - - -
73C ARG* 2.8 54.2 + - - +
75C ASN* 4.5 12.8 - - + +
361C LEU 2.7 21.6 + - - -
362C SER* 3.4 11.5 - - - +
365C THR* 2.7 27.3 + - - -
366C ALA* 3.2 27.8 + - + -
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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