Contacts of the strand formed by residues 46 - 50 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ARG* 3.9 0.2 - - - -
44D ASN 3.9 2.2 + - - -
45D THR* 1.3 76.3 + - - +
47D ILE* 1.3 61.5 + - - +
48D ILE 4.1 0.2 - - - -
70D ASN* 3.4 11.9 - - - -
71D VAL* 6.5 0.2 - - - -
357D ASP 3.1 11.3 + - - -
358D CYS* 3.4 18.4 - - - -
359D ILE* 3.0 26.9 + - - +
464D HIS 4.0 9.4 + - - -
466D TYR 5.7 0.2 + - - -
467D ARG* 5.6 0.4 - - - +
1004D GOL 4.2 5.7 - - - -
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ARG* 3.3 37.0 - - - +
45D THR* 4.2 0.4 - - - +
46D GLY* 1.3 75.2 - - - +
48D ILE* 1.3 66.6 + - - +
49D CYS* 3.8 23.1 - - - -
68D GLY 3.5 16.4 - - - +
69D MET* 3.9 1.9 - - - -
70D ASN* 2.8 37.9 + - - +
71D VAL 3.2 6.2 + - - +
359D ILE 3.7 2.9 - - - +
361D LEU* 4.8 2.7 - - + -
375D VAL* 4.1 10.1 - - + +
378D GLN* 3.9 26.0 - - + +
379D HIS* 3.8 30.5 - - + +
382D ALA* 5.6 0.2 - - + -
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 1.3 75.2 - - - +
49D CYS* 1.3 60.5 + - - +
71D VAL* 3.5 35.9 - - + +
73D ARG* 4.1 16.8 - - + -
241D PHE* 4.1 13.2 - - + -
325D ILE* 3.7 38.4 - - + -
358D CYS* 4.0 21.8 - - + -
359D ILE 2.9 14.0 + - - +
360D MET* 3.7 17.5 - - + -
361D LEU* 2.7 35.3 + - - +
465D LEU* 4.4 5.2 - - + -
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Residues in contact with CYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 3.8 16.8 - - - -
48D ILE* 1.3 78.6 - - - +
50D THR* 1.3 56.7 + - - +
51D ILE* 3.5 2.5 + - + +
64D MET* 3.7 11.7 - - + -
69D MET* 3.6 33.7 - - - -
71D VAL 2.9 7.5 + - - -
72D ALA* 3.5 5.2 - - - -
73D ARG* 2.8 31.7 + - - -
361D LEU* 4.0 4.9 - - - -
365D THR* 3.8 10.5 - - - +
375D VAL* 3.6 30.1 - - - -
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Residues in contact with THR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D CYS* 1.3 70.1 - - - +
51D ILE* 1.3 64.8 + - - +
55D SER* 3.9 0.2 + - - -
73D ARG* 2.7 56.6 + - - +
75D ASN* 4.5 12.6 - - + +
361D LEU 2.7 24.4 + - - -
362D SER* 3.6 9.6 - - - +
365D THR* 2.8 23.3 + - - +
366D ALA* 3.2 29.3 + - + -
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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