Contacts of the helix formed by residues 82 - 97 (chain C) in PDB entry 4QKB
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 SER 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C THR* 5.0 0.3 - - - +
51C GLU* 2.7 36.1 + - - -
81C TRP* 1.3 76.5 - - - +
83C GLU* 1.3 59.3 + - - +
84C ALA* 3.8 7.4 + - - +
85C SER 3.3 8.8 + - - -
86C MSE 2.8 28.4 + - - +
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Residues in contact with GLU 83 (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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82C SER* 1.3 71.5 - - - +
84C ALA* 1.3 64.5 + - - +
86C MSE 3.7 7.7 - - - +
87C ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 84 (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 THR* 3.6 25.8 - - + +
82C SER* 3.8 5.1 + - - +
83C GLU* 1.3 79.0 - - - +
85C SER* 1.3 60.4 + - - +
87C ALA* 3.4 19.2 + - - +
88C ILE* 3.5 13.9 + - - +
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.7 9.9 - - - +
48C LEU* 4.0 11.2 - - - +
51C GLU* 2.5 34.0 + - - +
81C TRP* 3.4 27.6 - - - -
82C SER* 3.3 8.8 + - - -
84C ALA* 1.3 75.6 - - - +
86C MSE 1.3 59.5 + - - +
88C ILE* 3.6 11.1 + - - +
89C MSE 3.1 32.2 + - - +
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Residues in contact with MSE 86 (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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79C SER 4.8 7.6 - - - +
81C TRP* 3.6 40.6 - - + +
82C SER 2.8 22.0 + - - +
83C GLU* 3.7 8.5 - - - +
85C SER* 1.3 70.6 - - - +
87C ALA* 1.3 64.6 + - - +
89C MSE 3.8 7.6 - - - +
90C ARG* 3.1 62.3 + - - +
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Residues in contact with ALA 87 (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 GLU* 5.8 0.4 - - - +
83C GLU 3.1 13.9 + - - +
84C ALA* 3.4 13.2 - - - +
85C SER 3.3 0.2 - - - -
86C MSE 1.3 77.6 - - - +
88C ILE* 1.3 62.2 + - + +
90C ARG* 3.4 7.0 + - - +
91C ARG* 3.1 27.1 + - - +
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Residues in contact with ILE 88 (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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39C PHE* 5.3 0.4 - - + -
40C LEU* 3.5 26.9 - - + -
44C GLU* 3.6 54.7 + - + +
47C THR* 4.2 11.7 - - + +
48C LEU* 4.0 20.4 - - + -
84C ALA 3.5 16.8 + - - +
85C SER* 3.8 5.8 - - - +
86C MSE 3.4 0.2 - - - -
87C ALA* 1.3 73.8 - - + +
89C MSE 1.3 66.8 + - - +
91C ARG* 3.2 9.2 + - + +
92C VAL* 3.0 21.9 + - + +
135C LEU* 4.2 16.8 - - + -
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Residues in contact with MSE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 5.2 4.3 - - - -
81C TRP* 3.9 43.7 - - + +
85C SER 3.1 19.1 + - - +
86C MSE 3.8 15.3 - - - +
87C ALA 3.3 0.2 - - - -
88C ILE* 1.3 79.1 - - - +
90C ARG* 1.3 59.2 + - + +
92C VAL* 3.1 25.8 + - + +
93C GLN* 3.0 25.5 + - - +
107C VAL* 4.5 8.5 - - + -
135C LEU* 4.1 11.0 - - + -
200C VAL* 3.8 20.6 - - + +
202C CYS* 3.5 30.2 - - - -
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Residues in contact with ARG 90 (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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86C MSE 3.1 43.9 + - - +
87C ALA* 3.8 6.0 - - - +
89C MSE 1.3 77.7 - - + +
91C ARG* 1.3 59.1 + - - +
93C GLN* 3.3 12.5 + - - +
94C ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 91 (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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36C ARG* 5.4 1.8 - - - +
39C PHE* 2.7 60.9 + - + +
40C LEU* 4.4 1.4 - - - +
44C GLU* 2.8 49.1 + - - -
87C ALA 3.1 16.7 + - - +
88C ILE* 3.3 11.2 - - - +
90C ARG* 1.3 75.9 - - - +
92C VAL* 1.3 55.9 + - - +
94C ALA* 3.4 5.5 + - - +
95C ALA* 2.9 31.5 + - - +
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Residues in contact with VAL 92 (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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39C PHE* 3.9 21.1 - - + -
88C ILE 3.0 16.5 + - - +
89C MSE 3.1 14.1 + - + +
91C ARG* 1.3 73.0 - - - +
93C GLN* 1.3 61.4 + - - +
95C ALA* 3.1 2.4 + - - +
96C ALA* 2.9 30.5 + - - +
97C PHE* 4.7 0.7 - - + -
133C ALA* 4.3 15.0 - - + +
135C LEU* 3.8 32.8 - - + -
164C LEU* 4.0 15.7 - - + -
202C CYS* 4.1 25.1 - - + -
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Residues in contact with GLN 93 (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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89C MSE 3.0 12.8 + - - +
90C ARG* 3.3 15.7 + - - +
92C VAL* 1.3 75.0 - - - +
94C ALA* 1.3 57.9 - - - +
97C PHE* 2.8 48.0 + - + +
99C PRO 3.8 20.6 + - - -
101C GLN 3.9 12.3 + - - -
103C LEU* 3.4 34.0 - - + +
202C CYS* 6.3 0.7 - - - -
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Residues in contact with ALA 94 (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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90C ARG 2.9 18.3 + - - +
91C ARG* 3.8 6.5 - - - +
93C GLN* 1.3 76.6 - - - +
95C ALA* 1.3 60.7 + - - +
97C PHE 4.4 7.2 - - - +
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Residues in contact with ALA 95 (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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36C ARG* 3.7 27.7 + - - +
39C PHE* 3.7 15.7 - - + -
91C ARG 2.9 18.2 + - - +
92C VAL 3.1 4.0 + - - +
94C ALA* 1.3 76.6 - - - +
96C ALA* 1.3 58.2 + - - +
164C LEU* 4.4 7.2 - - + -
166C ILE* 3.8 10.9 - - - +
168C ARG* 5.1 2.6 + - - -
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Residues in contact with ALA 96 (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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92C VAL* 2.9 15.3 + - + +
95C ALA* 1.3 80.9 - - + +
97C PHE* 1.3 63.0 + - + +
131C THR* 3.6 11.5 - - + +
133C ALA* 3.7 28.9 - - + -
164C LEU* 5.3 1.8 - - + -
166C ILE* 3.7 22.2 - - + -
168C ARG* 2.7 28.5 + - - +
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Residues in contact with PHE 97 (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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92C VAL* 4.7 1.3 - - + -
93C GLN* 2.8 48.2 + - + +
94C ALA* 4.4 7.1 - - - +
96C ALA* 1.3 79.5 - - + +
98C GLY* 1.3 69.0 + - - +
99C PRO 4.1 1.3 - - - +
101C GLN* 4.0 14.1 - - + +
103C LEU* 3.7 20.6 - - + -
131C THR* 3.3 33.2 - - + -
133C ALA* 3.7 23.8 - - + -
168C ARG* 5.2 0.7 - - - -
202C CYS* 3.4 40.4 - - + -
203C ARG 3.9 1.1 - - - -
204C SER* 3.4 26.5 - - - -
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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