Contacts of the helix formed by residues 75 - 89 (chain A) in PDB entry 1W3U
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 1.3 76.9 - - - +
76A GLY* 1.3 63.9 + - - +
78A SER* 4.2 4.5 + - - -
79A THR* 2.6 32.6 + - - -
203A GLY* 5.1 3.2 + - - -
1363A PLP 4.5 0.5 + - - -
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN 4.7 0.7 - - - +
75A GLY* 1.3 78.7 - - - +
77A ALA* 1.3 67.1 + - - -
78A SER 3.1 2.2 - - - -
79A THR* 3.1 6.2 + - - -
80A GLN* 3.5 8.0 + - - +
194A GLY* 5.0 1.3 - - - -
196A GLN* 5.6 0.7 - - - -
203A GLY* 6.0 2.0 - - - -
204A VAL 5.6 0.8 - - - -
205A THR* 3.0 28.2 + - - +
1363A PLP 3.2 18.2 - - - -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY* 1.3 72.8 - - - -
78A SER* 1.3 64.2 + - - +
80A GLN* 2.9 14.5 + - - +
81A PHE* 3.1 15.7 + - - -
175A SER* 3.3 27.1 - - - +
192A TYR* 3.9 22.0 - - + -
194A GLY* 4.1 6.6 - - - +
205A THR* 3.8 6.4 + - - +
1363A PLP 3.2 32.4 + - + +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.4 3.6 - - - -
76A GLY 3.1 0.2 - - - -
77A ALA* 1.3 78.8 - - - +
79A THR* 1.3 61.4 + - - +
81A PHE* 3.2 37.2 + - - +
82A ALA* 3.9 3.1 + - - +
103A TRP* 4.5 5.2 - - - -
110A GLU* 4.7 4.0 - - - +
1363A PLP 2.6 33.2 + - - -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 5.7 0.9 - - + -
74A GLN 4.2 11.2 - - - +
75A GLY* 2.6 34.2 + - - -
76A GLY 3.1 3.1 + - - -
77A ALA 3.1 0.6 - - - -
78A SER* 1.3 75.6 - - - +
80A GLN* 1.3 68.5 + - - +
82A ALA* 3.0 9.6 + - + +
83A MET* 2.8 24.7 + - + +
225A LEU* 4.4 21.5 - - + -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.9 21.8 - - - +
74A GLN 5.1 0.6 + - - -
76A GLY 3.5 2.5 + - - +
77A ALA 2.9 9.2 + - - +
79A THR* 1.3 79.0 - - - +
81A PHE* 1.3 68.0 + - - +
83A MET* 3.4 25.7 - - - +
84A ILE* 2.9 35.5 + - + +
190A LEU* 4.9 0.2 - - - +
192A TYR* 3.4 32.2 - - + +
205A THR* 3.9 19.4 - - + +
207A VAL* 3.6 16.2 - - + +
227A TYR* 2.5 32.8 + - - -
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 3.1 14.6 + - - -
78A SER* 3.3 27.1 - - - +
79A THR 3.1 0.4 - - - -
80A GLN* 1.3 77.2 - - - +
82A ALA* 1.3 57.0 + - - +
84A ILE* 5.2 1.1 - - - -
85A PRO* 3.0 22.2 - - - +
97A TYR* 4.7 1.6 + - - -
103A TRP* 3.6 35.9 - + - -
106A LYS* 3.6 31.6 - - + -
107A ALA* 3.6 23.3 - - + +
110A GLU* 3.5 26.4 - - + +
111A ALA 4.3 1.4 + - - -
147A HIS* 4.9 0.4 - - - -
173A ASP* 3.4 13.7 - - - -
192A TYR* 3.2 27.8 - + - -
1363A PLP 3.7 11.4 - + - -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 3.9 2.0 + - - +
79A THR* 3.0 10.5 + - + +
80A GLN 3.0 0.2 - - - -
81A PHE* 1.3 79.6 - - - +
83A MET* 1.3 61.5 + - - +
84A ILE 3.2 1.6 - - - -
85A PRO* 3.2 6.6 - - - +
86A MET* 2.9 46.0 + - - +
110A GLU* 4.2 19.7 - - + +
114A ILE* 5.0 8.5 - - + -
225A LEU* 6.3 0.7 - - + -
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Residues in contact with MET 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.1 8.5 - - + -
79A THR* 2.8 17.9 + - - +
80A GLN* 3.4 25.1 - - - +
82A ALA* 1.3 79.1 - - - +
84A ILE* 1.3 62.7 + - - +
86A MET* 4.1 9.0 - - - -
87A ASN* 2.9 32.1 + - - +
224A MET 4.4 2.7 - - - +
225A LEU* 3.5 51.8 - - + +
226A ARG 3.6 12.3 - - - +
227A TYR* 3.4 36.5 - - + +
230A TYR* 3.7 15.3 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLN* 2.9 20.5 + - + +
81A PHE* 5.2 0.9 - - - -
83A MET* 1.3 76.2 - - - +
85A PRO* 1.3 66.4 - - + +
87A ASN 3.1 1.7 + - - -
88A PHE* 2.9 34.9 + - + +
97A TYR* 5.0 0.4 - - - +
145A TYR* 3.8 16.8 - - + +
147A HIS* 4.5 5.2 - - + -
171A ILE* 3.7 35.4 - - + -
190A LEU* 4.0 10.1 - - + -
192A TYR* 3.3 44.2 - - + +
227A TYR* 3.2 23.1 - - + +
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Residues in contact with PRO 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE 3.0 29.2 - - - +
82A ALA 3.2 11.4 - - - +
84A ILE* 1.3 91.7 - - + +
86A MET* 1.3 57.8 + - - +
89A LEU* 2.8 49.0 + - + +
97A TYR* 4.4 2.2 - - - +
111A ALA* 3.9 17.7 - - - -
114A ILE* 3.7 22.1 - - + +
145A TYR* 3.2 23.8 - - + +
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Residues in contact with MET 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 2.9 37.0 + - - +
83A MET* 3.6 9.9 - - - +
85A PRO* 1.3 75.7 - - - +
87A ASN* 1.3 62.5 + - - +
89A LEU 4.8 1.7 + - - +
114A ILE* 3.8 29.1 - - + +
218A PRO* 3.8 7.8 - - - +
220A HIS* 4.9 3.5 + - - -
221A LEU* 3.4 44.2 - - + +
222A PRO* 4.6 6.7 - - + -
225A LEU* 3.7 34.3 - - + +
1364A GOL 4.8 6.7 - - - +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET* 2.9 34.2 + - - +
84A ILE 3.8 1.1 - - - +
86A MET* 1.3 80.9 - - - +
88A PHE* 1.3 71.5 + - + +
89A LEU 5.6 0.4 - - - -
90A LYS* 5.1 8.0 - - - +
214A VAL* 5.5 0.7 - - - +
217A SER* 3.5 19.8 + - - -
218A PRO* 3.5 22.0 - - - +
221A LEU* 3.8 5.2 - - - +
225A LEU 2.7 26.8 + - - -
226A ARG* 3.6 1.2 - - - -
227A TYR* 3.0 44.6 + - + -
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 2.9 23.5 + - + +
87A ASN* 1.3 86.5 - - + +
89A LEU* 1.3 62.0 + - - +
90A LYS* 3.1 20.0 + - - +
93A GLN* 3.3 12.6 - - - +
144A ALA* 3.4 13.4 - - - +
145A TYR* 3.7 16.8 - - + -
169A PRO* 6.3 3.8 - - + -
171A ILE* 3.9 23.1 - - + -
190A LEU* 3.8 26.9 - - + -
209A VAL* 4.6 3.6 - - + -
213A LEU* 3.6 35.9 - - + -
214A VAL* 3.5 22.7 - - + -
227A TYR* 3.8 14.4 - + - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PRO* 2.8 37.7 + - + +
86A MET 5.4 1.2 - - - +
87A ASN 3.8 0.4 - - - -
88A PHE* 1.3 72.2 - - - +
90A LYS* 1.3 62.3 + - - +
91A GLU 3.8 0.2 + - - -
93A GLN 3.3 30.5 - - - +
94A THR 3.9 0.9 - - - -
95A ALA* 3.5 30.3 - - + +
111A ALA 4.1 8.1 - - - +
114A ILE* 4.2 8.2 - - + +
115A GLY* 3.4 42.8 - - - +
116A ASP 3.7 6.5 - - - +
144A ALA* 4.0 6.1 - - + -
145A TYR* 4.5 3.6 - - + -
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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