Contacts of the helix formed by residues 75 - 92 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ASN* 3.9 0.2 - - - +
412C TRP* 3.9 9.0 - - - -
73D THR 3.4 0.8 + - - -
74D PHE* 1.3 67.1 - - - +
76D VAL* 1.3 64.5 + - - -
77D GLY 3.3 0.9 - - - -
78D GLU* 2.8 15.9 + - - -
79D LEU* 3.0 31.2 + - - +
115D HIS 3.9 6.3 - - - -
125D PHE* 3.6 28.5 - - - -
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASN* 3.4 12.8 + - - +
412C TRP* 3.2 50.0 - - + +
414C SER* 3.7 13.0 - - - +
600C TPP 3.3 33.4 - - + +
73D THR* 3.7 7.2 - - + -
74D PHE 2.9 6.7 + - - -
75D GLY* 1.3 72.6 - - - -
77D GLY* 1.3 59.7 + - - +
80D SER* 2.8 25.6 + - - -
115D HIS* 3.4 30.3 - - + +
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Residues in contact with GLY 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D GLU* 3.6 29.6 - - - +
72D THR* 3.6 11.2 - - - -
73D THR* 3.0 17.4 + - - -
76D VAL* 1.3 79.7 - - - +
78D GLU* 1.3 67.2 + - - +
80D SER* 3.1 14.9 + - - -
81D ALA* 3.3 9.4 + - - +
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Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D THR* 3.3 17.3 + - - +
73D THR 3.0 6.9 + - - +
74D PHE* 3.5 11.6 - - - -
75D GLY* 2.8 31.4 + - - +
77D GLY* 1.3 77.0 - - - +
79D LEU* 1.3 66.6 + - + +
81D ALA* 3.1 11.4 + - - +
82D LEU* 3.2 21.8 - - + +
97D HIS* 3.8 15.0 - - + -
99D VAL* 3.6 10.2 - - + +
125D PHE* 3.3 31.0 - - + +
129D SER* 4.7 1.1 + - - +
164D TYR* 2.5 35.1 + - + -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU 4.4 7.8 - - - +
80C SER 5.5 0.5 - - - +
82C LEU* 4.2 10.1 - - + +
83C ASN* 3.9 21.2 + - + +
86C ALA* 3.4 33.2 - - + -
132C ILE* 5.0 0.2 - - + -
412C TRP* 4.1 2.9 - - + -
75D GLY 3.0 20.5 + - - +
78D GLU* 1.3 78.9 - - + +
80D SER* 1.3 64.8 + - - +
81D ALA 3.3 0.7 + - - -
82D LEU* 3.4 31.8 + - + +
125D PHE* 3.7 39.9 - - + +
128D MET* 4.0 28.0 - - + -
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 4.1 17.4 - - - +
79C LEU 5.5 1.0 - - - +
80C SER* 5.3 6.7 - - - +
83C ASN* 3.1 23.1 + - - +
600C TPP 4.3 2.4 - - - +
51D GLU* 3.7 20.6 + - - -
52D LEU* 3.4 28.6 - - - +
76D VAL 2.8 19.0 + - - -
77D GLY 3.1 11.2 + - - -
79D LEU* 1.3 79.7 - - - +
81D ALA* 1.3 58.8 + - - +
82D LEU 3.6 0.7 + - - -
83D ASN* 4.8 0.9 + - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D GLU* 3.9 20.2 - - - +
52D LEU* 4.3 1.6 - - - +
55D ALA* 3.7 10.3 - - + +
70D ILE* 4.1 12.3 - - + -
72D THR* 4.4 1.6 - - + -
77D GLY 3.3 9.1 + - - +
78D GLU 3.1 10.3 + - - +
80D SER* 1.3 77.6 - - - +
82D LEU* 1.3 64.6 + - - +
83D ASN 3.3 2.5 - - - -
84D GLY* 2.9 16.1 + - - -
85D ILE* 3.0 12.5 + - + +
97D HIS* 4.1 15.3 - - + +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 4.6 11.7 - - + +
82C LEU* 5.8 4.3 - - + -
128C MET* 3.8 27.4 - - + -
78D GLU* 3.2 24.2 - - + +
79D LEU* 3.4 30.2 + - + +
80D SER 3.4 3.6 - - - -
81D ALA* 1.3 79.7 - - - +
83D ASN* 1.3 58.5 + - - +
85D ILE* 3.2 12.7 + - + -
86D ALA* 2.7 31.4 + - - +
97D HIS* 4.4 5.2 - - + -
128D MET* 4.6 4.0 - - + -
129D SER* 3.3 31.9 - - - +
132D ILE* 3.6 15.2 - - + +
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLY 3.9 1.6 - - - +
76C VAL* 3.4 13.5 + - - -
79C LEU* 3.9 12.1 + - + +
80C SER* 3.0 36.8 + - - +
52D LEU* 3.9 7.6 - - + +
56D TYR* 2.9 16.5 + - - -
80D SER 4.8 0.6 + - - -
81D ALA 3.3 1.0 - - - -
82D LEU* 1.3 77.7 - - - +
84D GLY* 1.3 61.2 + - - +
86D ALA* 4.0 1.9 - - - +
87D GLY* 3.2 16.5 + - - -
412D TRP* 3.1 29.1 + - - -
414D SER* 2.9 27.5 + - - -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.5 6.2 - - - +
55D ALA* 3.8 19.5 - - - -
56D TYR* 4.0 22.7 - - - -
59D ASP* 4.6 1.9 - - - +
81D ALA 2.9 8.1 + - - -
83D ASN* 1.3 75.5 - - - +
85D ILE* 1.3 64.8 + - - +
87D GLY* 3.2 3.3 + - - -
88D SER* 3.0 25.1 + - - -
409D GLN* 5.8 0.3 + - - -
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ALA* 4.6 7.0 - - + -
70D ILE* 4.2 13.9 - - + -
81D ALA* 3.0 18.4 + - + +
82D LEU* 3.2 10.1 + - + +
84D GLY* 1.3 76.1 - - - +
86D ALA* 1.3 56.5 + - - +
88D SER* 3.1 8.3 + - - +
89D TYR* 2.9 24.4 + - - +
95D VAL* 4.2 15.0 - - + -
97D HIS* 3.8 42.8 - - + +
129D SER* 5.6 1.8 - - - +
132D ILE* 3.8 25.8 - - + +
133D SER* 5.0 3.8 - - - +
162D PRO* 3.5 23.0 - - + +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 3.3 33.7 - - + -
117C LEU* 3.8 5.2 - - + +
82D LEU 2.7 14.2 + - - +
83D ASN 4.0 0.9 - - - +
85D ILE* 1.3 72.9 - - - +
87D GLY* 1.3 58.0 + - - +
89D TYR* 3.2 3.6 + - - +
90D ALA* 2.8 29.1 + - - +
132D ILE* 3.8 24.1 - - + +
412D TRP* 3.7 16.2 - - + -
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ASP* 4.2 4.0 - - - -
83D ASN 3.2 7.4 + - - -
84D GLY* 3.2 6.3 + - - -
86D ALA* 1.3 76.5 - - - +
88D SER* 1.3 58.3 + - - +
90D ALA* 4.3 0.2 - - - -
91D GLU* 2.9 36.8 + - - +
409D GLN* 4.3 5.2 - - - -
412D TRP* 3.2 34.7 - - - +
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Residues in contact with SER 88 (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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55D ALA 4.8 0.9 + - - -
59D ASP* 2.7 31.1 + - - +
84D GLY 3.0 14.4 + - - -
85D ILE* 3.4 10.4 - - - +
87D GLY* 1.3 74.1 - - - +
89D TYR* 1.3 64.4 + - - +
92D HIS* 3.0 4.2 + - - -
93D VAL* 2.8 41.2 + - - +
95D VAL* 3.5 16.1 - - - +
162D PRO* 3.6 15.9 - - - +
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Residues in contact with TYR 89 (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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117C LEU* 4.0 34.8 - - + -
119C ASN* 4.7 12.2 + - + +
85D ILE 2.9 8.8 + - - +
86D ALA* 3.2 10.7 + - - +
88D SER* 1.3 77.8 - - - +
90D ALA* 1.3 65.0 + - - +
91D GLU 3.2 0.5 + - - -
92D HIS 3.3 4.5 + - - -
131D ASN 5.2 3.4 - - - -
132D ILE* 3.3 33.7 - - + +
133D SER 3.7 25.1 + - - -
134D GLU* 3.9 6.4 + - - -
161D ARG* 2.9 70.1 + - - +
162D PRO* 3.4 13.4 - - + +
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Residues in contact with ALA 90 (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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116C THR 3.5 24.2 - - - +
117C LEU* 3.8 18.7 - - - +
86D ALA 2.8 20.0 + - - +
87D GLY 3.7 4.7 - - - +
89D TYR* 1.3 74.0 - - - +
91D GLU* 1.3 59.4 + - - +
92D HIS* 3.3 15.6 + - - -
288D LEU* 4.6 1.9 - - - +
411D LEU* 3.4 22.2 - - + +
412D TRP* 3.8 18.2 - - + -
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 2.9 30.9 + - - +
87D GLY 2.9 18.7 + - - +
89D TYR 3.2 0.2 - - - -
90D ALA* 1.3 77.9 - - + +
92D HIS* 1.3 66.3 + - - +
93D VAL* 3.5 3.4 - - + -
224D ARG* 3.0 28.2 - - - +
247D MET* 3.5 25.0 - - + +
288D LEU* 5.6 0.9 - - - +
408D SER 4.0 2.8 - - - +
409D GLN* 3.1 29.5 - - + -
411D LEU* 2.9 15.6 + - + +
412D TRP* 2.9 30.4 + - + +
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Residues in contact with HIS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU 5.6 0.2 + - - -
88D SER 3.0 5.0 + - - -
89D TYR 3.3 3.9 + - - -
90D ALA 3.3 17.7 + - - -
91D GLU* 1.3 81.4 - - - +
93D VAL* 1.3 58.2 + - - +
159D THR 5.1 0.6 + - - -
160D GLN* 2.7 24.1 + - - +
161D ARG* 3.1 35.8 + - - -
221D CYS* 4.3 3.3 - - - -
224D ARG* 2.8 27.6 + - + +
225D HIS* 2.9 30.5 + + - +
288D LEU* 4.4 10.3 - - + +
603D PY0 3.3 36.1 + - + +
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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
------------------------------------------------------------
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