Contacts of the helix formed by residues 75 - 91 (chain C) in PDB entry 2W93
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 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR 3.4 0.6 + - - -
74C PHE* 1.3 68.8 - - - +
76C VAL* 1.3 58.8 + - - -
77C GLY 3.3 1.1 - - - -
78C GLU* 2.9 16.1 + - - -
79C LEU* 2.9 36.7 + - - +
115C HIS 3.8 6.1 - - - -
125C PHE* 3.7 29.1 - - - -
412D TRP* 3.9 8.7 - - - -
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 3.7 6.1 - - + -
74C PHE 2.9 6.9 + - - -
75C GLY* 1.3 71.9 - - - -
77C GLY* 1.3 61.1 + - - +
80C SER* 2.8 26.3 + - - -
115C HIS* 3.4 32.1 - - + +
83D ASN* 3.4 12.1 + - - -
412D TRP* 3.2 49.4 - - + +
414D SER* 3.8 15.3 - - - +
600D TPP 3.3 32.6 - - + +
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.6 30.2 - - - +
72C THR* 3.6 10.5 - - - -
73C THR* 3.0 17.8 + - - -
76C VAL* 1.3 80.5 - - - +
78C GLU* 1.3 66.2 + - - +
80C SER* 3.2 13.2 + - - -
81C ALA* 3.3 10.6 + - - +
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C THR* 3.3 17.1 + - - +
73C THR 3.1 5.6 + - - +
74C PHE* 3.5 12.0 - - - -
75C GLY* 2.9 29.9 + - - +
77C GLY* 1.3 76.1 - - - +
79C LEU* 1.3 66.9 + - + +
81C ALA* 3.1 11.8 + - - +
82C LEU* 3.2 21.3 + - + +
97C HIS* 3.7 15.5 - - + -
99C VAL* 3.6 11.5 - - + +
125C PHE* 3.4 30.7 - - + +
129C SER* 4.6 1.0 + - - -
164C TYR* 2.6 35.6 + - + -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLY 2.9 21.2 + - - +
78C GLU* 1.3 77.0 - - + +
80C SER* 1.3 61.9 + - - +
81C ALA 3.3 0.5 + - - -
82C LEU* 3.4 31.4 + - + +
125C PHE* 3.6 37.9 - - + +
128C MET* 3.8 30.5 - - + -
79D LEU 4.4 7.6 - - - +
80D SER 5.5 0.7 - - - +
82D LEU* 4.3 8.1 - - + +
83D ASN* 3.9 22.3 + - + +
86D ALA* 3.3 34.5 - - + -
412D TRP* 4.0 3.6 - - + -
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.7 21.0 + - - -
52C LEU* 3.5 27.4 - - - +
76C VAL 2.8 22.8 + - - -
77C GLY 3.2 7.1 + - - -
79C LEU* 1.3 78.2 - - - +
81C ALA* 1.3 59.0 - - - +
82C LEU 3.4 0.7 + - - -
83C ASN* 4.7 1.0 + - - +
52D LEU* 4.1 17.7 - - - +
79D LEU 5.5 1.2 - - - +
80D SER* 5.3 6.5 - - - +
83D ASN* 3.0 22.9 + - - +
600D TPP 4.2 2.9 - - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.9 20.6 - - + +
52C LEU* 4.3 0.9 - - - +
55C ALA* 3.6 8.7 - - + +
70C ILE* 4.2 9.9 - - + -
72C THR* 4.4 2.2 - - + -
77C GLY 3.3 8.0 + - - +
78C GLU 3.1 11.0 + - - +
80C SER* 1.3 78.3 - - - +
82C LEU* 1.3 58.4 + - - +
83C ASN 3.3 2.7 - - - -
84C GLY* 2.8 24.0 + - - -
85C ILE* 3.0 12.1 + - + +
97C HIS* 4.1 17.0 - - + -
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 3.2 23.8 - - + +
79C LEU* 3.4 32.6 + - + +
80C SER 3.4 2.8 - - - -
81C ALA* 1.3 78.3 - - - +
83C ASN* 1.3 57.9 + - - +
85C ILE* 4.2 12.6 - - + -
86C ALA* 2.7 31.9 + - - +
97C HIS* 4.4 5.4 - - + -
125C PHE 5.4 0.2 - - - +
128C MET* 4.6 9.4 - - + -
129C SER* 3.3 27.4 - - - +
132C ILE* 3.6 15.0 - - + +
79D LEU* 4.2 11.8 - - + +
82D LEU* 5.8 3.4 - - + -
128D MET* 3.9 26.5 - - + -
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Residues in contact with ASN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.9 8.2 - - + +
56C TYR* 2.9 16.3 + - - -
80C SER 4.7 1.0 + - - -
81C ALA 3.3 0.8 - - - -
82C LEU* 1.3 76.9 - - - +
84C GLY* 1.3 61.8 + - - +
86C ALA* 4.0 0.2 - - - +
87C GLY* 3.2 16.5 + - - -
412C TRP* 3.0 34.4 + - - -
414C SER* 2.9 26.9 + - - -
75D GLY 3.9 1.4 - - - +
76D VAL* 3.4 15.0 + - - -
79D LEU* 3.9 12.0 + - + +
80D SER* 3.1 38.2 + - - +
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.6 6.2 - - - +
55C ALA* 3.6 21.9 - - - +
56C TYR* 4.0 20.1 - - - -
59C ASP* 4.6 2.1 - - - +
81C ALA 2.8 9.6 + - - -
83C ASN* 1.3 75.0 - - - +
85C ILE* 1.3 63.4 + - - -
87C GLY* 3.2 3.1 + - - -
88C SER* 3.1 25.4 + - - -
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 4.5 8.1 - - + +
70C ILE* 4.3 6.7 - - + -
81C ALA* 3.0 16.0 + - + +
82C LEU* 3.7 9.4 - - + +
84C GLY* 1.3 75.5 - - - +
86C ALA* 1.3 64.3 + - - +
88C SER* 3.1 7.1 + - - +
89C TYR* 2.9 19.6 + - - +
95C VAL* 4.1 23.6 - - + -
97C HIS* 3.8 41.3 - - + +
129C SER* 5.7 1.6 - - - +
132C ILE* 3.8 25.6 - - + +
133C SER* 5.0 3.6 - - - +
162C PRO* 3.6 22.6 - - + +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU 2.7 13.9 + - - +
83C ASN 4.0 0.7 - - - +
85C ILE* 1.3 74.3 - - - +
87C GLY* 1.3 58.6 + - - +
89C TYR* 3.2 2.8 + - - +
90C ALA* 2.8 30.1 + - - +
132C ILE* 3.8 24.4 - - + +
412C TRP* 3.6 17.5 - - + -
79D LEU* 3.4 33.4 - - + -
117D LEU* 3.7 4.4 - - + +
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Residues in contact with GLY 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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59C ASP* 4.2 5.3 - - - +
83C ASN 3.2 11.9 + - - -
84C GLY* 3.2 3.3 + - - -
86C ALA* 1.3 76.1 - - - +
88C SER* 1.3 57.7 + - - +
90C ALA* 3.8 0.2 - - - +
91C GLU* 3.0 36.2 + - - +
409C GLN* 4.2 6.0 + - - -
412C TRP* 3.3 34.7 - - - +
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA 4.7 0.9 + - - -
59C ASP* 2.7 35.1 + - - +
84C GLY 3.1 13.0 + - - -
85C ILE* 3.5 10.7 - - - -
87C GLY* 1.3 74.1 - - - +
89C TYR* 1.3 63.8 + - - +
92C HIS* 3.0 4.3 + - - -
93C VAL* 2.8 40.7 + - - +
95C VAL* 3.4 12.9 - - - +
162C PRO* 3.6 16.1 - - - +
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Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE 2.9 8.6 + - - +
86C ALA* 3.5 10.3 - - - +
88C SER* 1.3 79.3 - - - +
90C ALA* 1.3 58.8 + - - +
91C GLU 3.3 0.5 + - - -
92C HIS 3.3 4.7 + - - -
131C ASN 5.0 4.0 - - - -
132C ILE* 3.3 32.3 - - - +
133C SER* 3.9 24.2 + - - -
134C GLU* 4.0 9.5 + - - -
161C ARG* 2.8 68.1 + - - +
162C PRO* 3.4 12.5 - - + +
117D LEU* 3.9 38.4 - - + -
119D ASN* 4.9 11.3 + - + +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA 2.8 15.9 + - - +
87C GLY 3.8 4.7 - - - +
88C SER 3.3 0.2 - - - -
89C TYR* 1.3 78.6 - - - +
91C GLU* 1.3 58.2 + - - +
92C HIS* 3.3 14.7 + - - -
288C LEU* 4.4 1.7 - - - +
411C LEU* 3.3 22.9 - - + +
412C TRP* 3.9 16.8 - - + -
116D THR 3.6 24.5 - - - +
117D LEU* 3.8 18.9 - - - +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 2.8 31.6 + - - +
87C GLY 3.0 19.2 + - - +
90C ALA* 1.3 78.1 - - - +
92C HIS* 1.3 72.4 + - - +
93C VAL* 3.5 2.7 - - + -
224C ARG* 3.0 23.7 - - - +
247C MET* 4.8 9.4 - - - +
288C LEU* 5.1 5.9 - - - +
408C SER 4.1 2.6 - - - +
409C GLN* 3.1 25.7 - - + -
410C VAL 4.1 0.7 - - - -
411C LEU* 2.8 35.8 + - + -
412C TRP* 2.9 18.3 + - + +
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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
------------------------------------------------------------
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