Contacts of the helix formed by residues 74 - 91 (chain B) in PDB entry 1P3W
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 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 2.9 19.4 + - - -
73B SER* 1.3 83.5 + - - +
75B ALA* 1.3 60.6 + - - -
76B THR* 3.2 3.8 - - - -
77B GLU 3.2 2.9 + - - -
78B SER* 2.9 17.1 + - - -
212B GLY* 5.5 0.2 - - - -
213B ILE 3.7 15.7 - - - -
214B GLY* 3.6 4.2 - - - +
764B PLP 3.7 11.9 - - - -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY* 1.3 70.1 - - - -
76B THR* 1.3 59.9 + - - +
78B SER* 3.6 8.9 - - - -
79B ASP* 2.7 34.6 + - - +
182B THR* 3.1 27.6 - - - +
201B SER* 4.7 3.1 - - - -
202B PHE 3.9 9.3 + - - +
203B SER* 3.7 13.6 - - - -
764B PLP 3.2 29.3 + - + +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 4.2 5.6 - - + -
231A HIS 3.5 22.4 - - - +
232A GLY* 4.9 3.0 + - - +
240A ARG* 6.1 0.2 - - - -
241A SER* 3.8 22.7 - - - +
242A GLY* 3.6 15.1 - - - +
243A THR 4.5 0.2 + - - -
74B GLY* 3.2 0.8 - - - -
75B ALA* 1.3 80.0 - - - +
77B GLU* 1.3 56.2 + - - +
79B ASP* 3.5 2.4 - - - +
80B ASN* 2.7 36.7 + - - +
104B HIS* 4.7 2.3 + - - -
106B ALA* 3.8 16.2 - - + +
764B PLP 2.7 33.3 + - - -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 5.8 1.3 - - - -
230A MET* 3.8 29.4 - - + -
240A ARG* 4.8 1.1 + - - +
72B THR* 3.7 7.9 - - + -
73B SER* 2.6 51.2 + - - +
74B GLY* 3.2 7.3 + - - +
76B THR* 1.3 76.1 - - - +
78B SER* 1.3 61.9 + - - +
80B ASN* 3.2 1.1 + - - +
81B LEU* 2.7 34.4 + - + +
230B MET* 4.7 10.2 - - - +
240B ARG* 2.6 44.9 + - - +
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 2.8 28.6 + - - +
74B GLY 2.9 10.7 + - - -
75B ALA* 3.2 8.3 + - - -
77B GLU* 1.3 76.9 - - - +
79B ASP* 1.3 57.5 + - - +
81B LEU* 3.7 3.1 - - - +
82B ALA* 2.9 32.4 + - - +
201B SER* 3.5 18.8 + - - -
202B PHE 4.0 0.2 + - - -
215B ALA 2.8 31.3 + - - -
216B LEU* 4.0 7.7 - - - +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 2.7 22.5 + - - +
76B THR 3.5 4.7 - - - +
78B SER* 1.3 74.5 - - - +
80B ASN* 1.3 61.4 + - - +
83B ILE* 3.2 31.0 + - - +
104B HIS* 4.9 0.3 - - - -
106B ALA* 3.5 28.7 - - + +
107B VAL* 3.4 18.8 - - + +
110B THR* 4.5 0.2 - - - +
178B HIS* 3.4 11.8 - - - -
180B ASP* 2.7 25.7 - - - +
201B SER* 2.6 33.9 + - - -
764B PLP 3.9 2.8 - - - -
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 3.2 29.1 - - + +
231A HIS 2.8 44.0 - - - +
76B THR* 2.7 25.0 + - - +
77B GLU 3.5 4.5 - - - +
79B ASP* 1.3 76.2 - - - +
81B LEU* 1.3 58.1 + - - +
84B LYS* 2.9 64.5 + - + +
106B ALA 3.8 1.9 - - - +
110B THR* 3.3 16.7 + - - -
229B GLN* 5.0 1.6 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 4.4 11.0 - - + -
72B THR* 4.3 18.8 - - + -
77B GLU* 2.7 25.9 + - + +
78B SER 3.7 3.8 - - - +
80B ASN* 1.3 72.2 - - - +
82B ALA* 1.3 56.3 + - - +
85B GLY* 2.7 33.3 + - - -
216B LEU* 3.6 18.6 - - + -
226B ILE* 3.4 21.8 - - + +
227B GLU 4.0 15.3 - - - +
229B GLN* 4.2 21.3 - - + +
230B MET 6.1 0.2 - - - +
239B MET 3.8 22.9 - - - +
240B ARG* 4.5 6.1 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER 2.9 17.7 + - - +
79B ASP 4.1 0.9 - - - +
81B LEU* 1.3 76.2 - - - +
83B ILE* 1.3 59.1 + - - +
86B ALA* 3.0 32.3 + - - +
147B LEU* 4.8 0.2 - - - +
178B HIS* 3.5 32.8 - - + +
199B LEU* 3.5 15.1 - - + +
216B LEU* 3.7 21.0 - - + +
226B ILE* 4.3 2.4 - - - +
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP 3.2 19.1 + - - +
82B ALA* 1.3 77.2 - - - +
84B LYS* 1.3 58.9 + - - +
87B ALA* 2.9 33.1 + - - +
97B ILE* 4.8 2.0 - - + -
107B VAL* 3.6 42.4 - - + +
110B THR* 3.7 12.3 - - + -
111B CYS* 4.4 12.1 - - - -
114B LEU* 3.5 22.2 - - + -
147B LEU* 3.8 24.0 - - + +
149B SER* 3.7 15.0 - - - +
178B HIS* 4.0 16.2 - - + +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLN* 2.8 24.1 + - - +
230A MET* 5.6 0.4 - - + -
231A HIS* 2.8 35.5 + - - -
80B ASN* 2.9 40.6 + - + +
83B ILE* 1.3 75.1 - - - +
85B GLY* 1.3 60.9 + - - +
88B ASN* 2.9 39.6 + - - +
110B THR* 3.7 24.9 - - + +
113B GLN* 4.7 6.7 - - - +
114B LEU* 4.2 18.8 - - + -
117B GLU* 6.1 0.9 - - - +
229B GLN* 3.9 26.5 - - + +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU 2.7 23.4 + - - -
84B LYS* 1.3 79.1 - - - +
86B ALA* 1.3 59.1 + - - +
89B PHE* 3.2 14.6 + - - +
226B ILE* 3.5 9.6 - - - -
227B GLU* 2.9 41.5 + - - +
229B GLN* 4.1 2.1 - - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA 3.0 21.2 + - - +
83B ILE 4.3 0.7 - - - +
85B GLY* 1.3 72.7 - - - +
87B ALA* 1.3 65.9 + - - +
90B TYR* 3.0 43.4 + - + +
146B ILE* 4.6 1.8 - - - +
147B LEU* 4.4 16.2 - - + -
176B ILE* 4.5 6.3 - - + -
199B LEU* 3.9 17.7 - - + -
224B VAL* 5.9 0.2 - - + -
225B ARG 4.3 0.2 - - - -
226B ILE* 3.6 9.7 - - + +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE 2.9 19.9 + - - +
84B LYS* 3.9 2.5 - - - +
86B ALA* 1.3 77.3 - - - +
88B ASN* 1.3 57.6 + - - +
90B TYR 3.8 0.3 - - - -
91B GLN* 3.0 32.4 + - - +
97B ILE* 4.1 10.5 - - + -
114B LEU* 3.9 20.4 - - + -
119B PHE* 3.5 24.2 - - + -
146B ILE* 3.9 10.7 - - - +
147B LEU* 4.7 2.4 - - + +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 2.9 36.8 + - - +
87B ALA* 1.3 76.9 - - - +
89B PHE* 1.3 64.0 + - - +
91B GLN* 2.9 39.3 + - - +
114B LEU* 4.6 8.7 - - - +
117B GLU* 4.6 9.2 + - - +
119B PHE* 4.3 12.3 - - - -
227B GLU* 3.4 31.7 - - + +
229B GLN* 4.2 11.7 + - - +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLY 3.2 20.2 + - - +
86B ALA 3.3 3.6 + - - +
88B ASN* 1.3 79.9 - - - +
90B TYR* 1.3 90.0 + + - +
91B GLN* 3.8 0.7 + - - +
92B LYS* 5.0 3.3 + - - +
225B ARG* 3.6 49.6 - - + +
226B ILE* 4.0 8.5 - - - -
227B GLU* 3.7 22.1 - - + +
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ALA* 3.0 30.8 + - + +
87B ALA 3.8 1.8 - - - -
89B PHE* 1.3 98.4 - + - +
91B GLN* 1.3 58.2 + - - +
92B LYS* 3.1 3.6 - - - -
93B LYS* 2.8 63.1 + - + +
94B GLY 3.6 5.4 - - - +
146B ILE* 3.8 16.2 - - + +
176B ILE* 4.0 31.1 - - + +
223B ARG 4.3 3.6 + - - -
224B VAL* 3.6 10.6 - - + +
225B ARG* 2.8 45.7 + - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA 3.0 15.6 + - - +
88B ASN* 2.9 38.8 + - - +
89B PHE 3.5 1.0 - - - -
90B TYR* 1.3 76.7 - - - +
92B LYS* 1.3 70.6 + - + +
93B LYS 3.1 0.7 - - - -
94B GLY* 3.1 25.6 + - - +
95B LYS* 3.8 29.2 + - - +
119B PHE* 3.9 19.2 - - + -
227B GLU* 5.2 2.6 + - - -
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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
------------------------------------------------------------
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