Contacts of the helix formed by residues 82 - 95 (chain D) in PDB entry 2WLM
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D LEU* 4.2 5.8 - - - +
79D ARG* 3.2 40.7 + - - +
80D PRO 3.2 2.8 - - - -
81D GLY* 1.3 77.2 - - - +
83D PHE* 1.3 62.3 + - - +
84D THR* 4.0 1.3 + - - -
85D ASP* 2.9 34.1 + - - +
86D ALA* 3.2 17.7 + - - +
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Residues in contact with PHE 83 (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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62D ALA* 3.6 28.5 - - + -
65D ALA* 3.6 18.2 - - + -
66D LEU* 3.2 35.7 - - + -
69D LEU* 3.9 17.5 - - + +
81D GLY 4.1 2.0 + - - -
82D SER* 1.3 68.4 - - - +
84D THR* 1.3 61.1 + - - +
86D ALA* 3.1 2.5 + - - +
87D PHE* 2.6 52.3 + + + +
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Residues in contact with THR 84 (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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107C PRO* 5.8 8.5 - - + -
79D ARG* 4.1 13.6 + - - +
82D SER* 3.4 0.7 + - - -
83D PHE* 1.3 81.5 + - - +
85D ASP* 1.3 73.3 + - - +
87D PHE* 2.9 9.4 + - + +
88D PHE* 2.8 56.4 + - + -
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Residues in contact with ASP 85 (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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77D ASN 4.4 2.9 - - - +
78D ALA* 3.7 20.9 - - + -
79D ARG* 2.7 54.3 + - - +
82D SER* 2.9 23.7 + - - +
84D THR* 1.3 75.2 - - - +
86D ALA* 1.3 57.4 + - - +
88D PHE* 3.5 4.1 + - - -
89D PHE* 2.8 31.9 + - - +
102D LEU* 3.9 11.6 - - + +
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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
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65D ALA* 3.7 20.6 - - + +
68D TYR* 4.7 7.2 - - + -
69D LEU* 3.9 25.8 - - + -
75D ILE* 4.6 8.3 - - + -
78D ALA* 5.4 1.3 - - - +
82D SER 3.2 10.0 + - - +
83D PHE 3.1 7.3 + - - +
85D ASP* 1.3 78.1 - - - +
87D PHE* 1.3 59.1 + - - +
89D PHE* 3.3 10.0 + - - +
90D SER* 2.8 29.5 + - - -
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Residues in contact with PHE 87 (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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114C THR* 4.9 5.4 - - + -
58D LEU* 3.7 35.2 - - + -
61D ASN* 3.6 20.0 - - + -
62D ALA* 3.7 22.7 - - + -
65D ALA* 3.5 9.1 - - - +
83D PHE* 2.6 40.2 + + + +
84D THR* 2.9 5.5 + - - +
86D ALA* 1.3 71.5 - - - +
88D PHE* 1.3 84.1 + + - +
90D SER* 2.9 19.9 + - - -
91D VAL* 3.0 34.2 + - + +
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Residues in contact with PHE 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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107C PRO* 4.2 10.3 - - + -
110C ASN* 3.3 40.4 - - + -
111C THR* 3.6 19.3 - - + -
114C THR* 3.3 32.3 - - + -
84D THR* 2.8 52.9 + - + +
85D ASP* 4.0 4.9 - - - +
87D PHE* 1.3 88.3 - + - +
89D PHE* 1.3 55.5 + - - +
91D VAL* 3.1 6.5 - - + +
92D GLN* 2.6 46.6 + - - +
102D LEU* 5.1 3.4 - - + -
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Residues in contact with PHE 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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99A TYR* 3.4 30.5 - + - -
68D TYR* 3.6 30.7 - + - -
75D ILE* 2.9 36.1 - - + -
85D ASP 2.8 17.5 + - - +
86D ALA 3.4 3.4 - - - +
88D PHE* 1.3 75.9 - - - +
90D SER* 1.3 59.6 + - - +
92D GLN* 3.1 7.8 + - + +
93D THR* 2.8 32.4 + - - -
102D LEU* 3.3 55.3 - - + +
103D ILE 4.0 1.3 - - - -
104D PRO* 4.0 17.7 - - + -
113D VAL* 4.4 3.8 - - + -
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Residues in contact with SER 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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61D ASN* 2.5 47.8 + - - +
64D PHE* 3.7 0.8 - - - +
65D ALA 4.2 7.2 - - - -
68D TYR* 4.6 3.8 - - - -
86D ALA 2.8 13.0 + - - -
87D PHE* 3.1 12.1 - - - -
89D PHE* 1.3 79.8 - - - +
91D VAL* 1.3 55.2 + - - +
93D THR* 2.8 11.7 - - - +
94D MET 2.8 24.4 + - - -
116D GLU* 2.6 18.7 + - - +
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Residues in contact with VAL 91 (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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113C VAL* 5.6 1.6 - - + -
114C THR* 3.7 31.9 - - + -
117C ALA* 6.2 0.2 - - + -
57D TYR* 4.2 14.8 - - + +
58D LEU* 6.4 0.2 - - + -
61D ASN* 3.5 25.8 - - - +
87D PHE* 3.0 36.1 + - + +
88D PHE* 3.1 12.7 + - + +
90D SER* 1.3 70.7 - - - +
92D GLN* 1.3 68.5 + - + +
93D THR 2.9 1.9 + - - -
94D MET* 4.3 2.2 - - - +
95D ALA* 2.7 38.0 + - + +
97D ILE* 5.2 6.3 - - + -
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Residues in contact with GLN 92 (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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99A TYR* 5.6 1.6 - - + -
104C PRO* 4.5 1.6 - - - +
110C ASN* 4.1 15.4 + - - -
113C VAL* 5.3 3.2 - - - +
88D PHE* 2.6 37.4 + - - +
89D PHE* 3.5 8.4 - - + +
91D VAL* 1.3 81.4 - - + +
93D THR* 1.3 58.8 + - - +
96D THR* 3.3 0.5 + - - -
97D ILE* 2.8 40.7 + - + -
98D GLY* 2.9 18.4 + - - +
99D TYR* 3.2 46.7 + - + +
100D GLY 4.9 1.2 + - - -
101D LYS* 5.9 0.9 - - - +
102D LEU* 4.3 21.5 + - - +
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Residues in contact with THR 93 (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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97A ILE* 4.3 10.7 - - - +
99A TYR* 2.5 29.4 + - - -
68D TYR* 4.3 3.4 - - + +
89D PHE* 2.8 18.2 + - - -
90D SER* 2.8 15.5 - - - +
92D GLN* 1.3 78.0 - - - +
94D MET* 1.3 61.6 + - - +
96D THR* 3.0 24.0 + - - +
113D VAL* 3.7 16.6 + - - +
116D GLU* 2.7 38.4 - - + +
117D ALA* 4.8 3.5 - - - -
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Residues in contact with MET 94 (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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57D TYR* 3.3 24.2 - - + -
60D THR* 4.1 15.5 - - - +
61D ASN* 2.7 45.8 - - - +
64D PHE* 5.9 2.2 - - - -
90D SER 2.8 12.5 + - - +
91D VAL* 4.7 2.9 - - - -
93D THR* 1.3 76.7 - - - +
95D ALA* 1.3 59.5 + - - +
96D THR* 3.0 13.5 + - - +
116D GLU* 3.5 24.9 - - + +
117D ALA 4.7 1.2 - - - +
119D CYS* 5.3 3.8 - - - -
120D GLY* 3.4 39.5 - - - +
121D MET 5.0 0.3 + - - -
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Residues in contact with ALA 95 (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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96C THR* 3.9 15.6 + - + +
117C ALA* 4.2 20.9 - - + -
57D TYR* 4.7 10.1 - - + +
91D VAL 2.7 18.9 + - - +
94D MET* 1.3 73.0 - - - +
96D THR* 1.3 76.5 + - - +
97D ILE* 3.2 17.2 + - + -
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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