Contacts of the helix formed by residues 57 - 65 (chain C) in PDB entry 4QPL
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 TYR 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL 3.5 1.8 + - - -
45C HIS* 2.9 33.5 + - + +
47C VAL* 3.9 23.8 - - + -
55C PHE 3.4 0.6 + - - -
56C CYS* 1.3 70.1 - - - +
58C LEU* 1.3 66.2 + - + +
60C VAL* 3.2 5.6 + - + +
61C LYS* 2.9 54.5 + - + +
81C PHE* 5.5 1.1 - + - -
82C LEU* 2.7 47.5 + - + +
85C PRO* 4.0 9.2 - - + -
178C ALA* 3.4 26.9 - - + -
179C GLY* 4.1 11.3 + - - -
180C LEU* 3.7 32.3 - - + -
201C V3L 5.0 0.7 + - - -
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Residues in contact with LEU 58 (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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44C VAL* 4.9 1.7 + - + -
45C HIS* 5.8 2.7 - - + +
56C CYS* 3.2 5.3 - - + +
57C TYR* 1.3 94.5 - - + +
59C CYS* 1.3 57.3 + - - +
61C LYS* 3.8 7.2 - - + -
62C GLY* 2.9 21.5 + - - -
117C ASP* 3.7 30.1 - - + +
139C ILE* 4.5 9.4 - - + -
140C ALA* 3.3 32.8 - - + +
141C GLY 4.7 0.2 + - - -
178C ALA* 3.8 33.0 - - + +
201C V3L 3.9 22.0 - - + +
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Residues in contact with CYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C CYS* 3.9 2.5 - - - -
38C ILE* 4.0 29.4 - - + +
39C CYS* 3.7 15.7 - - - -
56C CYS* 3.2 11.5 + - - +
58C LEU* 1.3 77.3 - - - +
60C VAL* 1.3 65.4 + - - +
61C LYS 3.3 0.2 - - - -
62C GLY* 3.8 1.2 - - - +
63C ALA* 3.0 25.5 + - - +
202C ZN 2.4 37.5 - - - -
1D MET* 4.4 9.8 - - - +
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Residues in contact with VAL 60 (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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38C ILE* 4.9 3.1 - - + -
47C VAL* 3.9 16.4 - - + -
49C LEU* 4.8 5.8 - - + -
55C PHE* 3.7 28.5 - - + -
56C CYS 3.1 14.7 + - - +
57C TYR* 3.5 7.4 - - + +
59C CYS* 1.3 75.1 - - - +
61C LYS* 1.3 64.4 + - - +
63C ALA* 3.3 5.9 + - - +
64C SER* 2.9 23.6 + - - -
77C ILE* 4.6 22.2 - - + -
81C PHE* 4.6 15.3 - - + -
82C LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 61 (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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57C TYR* 2.9 44.8 + - + +
58C LEU* 3.7 15.9 - - + +
60C VAL* 1.3 77.2 - - - +
62C GLY* 1.3 60.8 + - - +
64C SER* 2.5 25.4 + - - -
65C TRP* 3.6 23.8 + - + -
82C LEU* 3.8 23.3 - - + +
140C ALA* 4.0 9.4 - - + -
178C ALA 5.3 0.2 + - - -
179C GLY* 5.1 0.2 - - - -
201C V3L 2.8 68.3 + - - -
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Residues in contact with GLY 62 (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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58C LEU 2.9 15.0 + - - -
59C CYS 3.4 1.5 + - - -
60C VAL 3.3 0.4 - - - -
61C LYS* 1.3 75.5 - - - +
63C ALA* 1.3 60.4 + - - +
65C TRP* 3.4 19.4 + - - +
66C LEU* 4.6 6.1 + - - +
140C ALA* 3.4 30.2 - - - +
141C GLY* 3.7 4.5 - - - -
1D MET* 3.7 13.5 - - - +
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Residues in contact with ALA 63 (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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38C ILE* 4.7 2.7 - - + -
59C CYS 3.0 16.9 + - - +
60C VAL* 3.9 5.2 - - - +
62C GLY* 1.3 74.6 - - - +
64C SER* 1.3 63.5 + - - +
65C TRP 3.3 0.9 - - - -
66C LEU* 3.2 15.4 + - - +
68C LYS* 3.3 29.7 + - + +
1D MET* 3.9 6.2 - - + -
62D PHE* 3.5 34.1 - - + -
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Residues in contact with SER 64 (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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60C VAL* 2.9 15.1 + - - -
61C LYS 2.5 20.4 + - - -
63C ALA* 1.3 73.8 - - - +
65C TRP* 1.3 70.9 + - - +
66C LEU 3.1 1.8 - - - -
67C GLY* 2.8 23.3 + - - +
68C LYS 4.7 3.8 - - - +
82C LEU* 3.3 28.1 - - - +
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Residues in contact with TRP 65 (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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61C LYS* 3.8 35.7 + - + -
62C GLY* 3.4 19.3 - - - +
63C ALA 3.3 0.8 - - - -
64C SER* 1.3 90.0 + - - +
66C LEU* 1.3 64.5 + - + +
67C GLY 3.3 0.6 + - - -
82C LEU* 5.4 3.8 - - + -
140C ALA* 2.8 23.7 + - + -
141C GLY* 4.8 1.1 - - - -
142C PHE* 3.2 32.4 - + + -
155C ARG* 4.3 8.7 - - - -
201C V3L 4.2 25.6 - - - -
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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