Contacts of the helix formed by residues 64 - 82 (chain B) in PDB entry 4D87
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 ALA 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ALA 3.4 22.9 - - - +
59B ALA 3.8 0.7 - - - +
62B SER 3.4 0.4 - - - -
63B SER* 1.3 72.6 - - - +
65B PHE* 1.3 67.6 + - - +
66B LEU 2.8 5.6 + - - -
67B PRO* 2.9 9.0 - - - +
68B TRP* 2.9 22.7 + - - +
250B TYR* 3.8 3.4 - - - +
259B GLY 3.8 12.3 - - - +
260B GLN* 2.7 23.1 - - - +
266B MET* 4.6 13.2 - - + -
273B PRO* 5.7 1.3 - - + -
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 2.7 27.0 + - - +
60B HIS* 4.3 2.0 - + - -
62B SER 3.9 9.6 + - - +
63B SER 3.6 0.2 - - - -
64B ALA* 1.3 74.3 - - - +
66B LEU* 1.3 87.9 + - + +
69B HIS* 2.7 52.3 + + + +
191B ARG* 4.0 6.3 - - + -
195B GLU* 3.3 50.7 - - + +
204B HIS* 2.9 43.7 - + - -
231B HIS* 4.1 8.1 - + - -
234B VAL* 4.4 14.4 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 2.8 4.2 + - - -
65B PHE* 1.3 98.7 - - + +
67B PRO* 1.3 62.7 - - + +
68B TRP 3.1 1.6 - - - -
69B HIS* 3.6 3.9 + - - +
70B ARG* 2.9 29.1 + - - +
177B TYR* 2.2 52.9 - - + +
190B PHE* 4.7 1.1 - - + -
191B ARG* 3.2 25.4 - - + -
194B LEU* 4.1 24.7 - - + -
234B VAL* 5.0 5.4 - - + -
238B TRP* 4.0 26.5 - - + +
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 2.9 27.8 - - - +
66B LEU* 1.3 87.8 - - + +
68B TRP* 1.3 64.4 + - - +
70B ARG* 3.2 9.9 - - + +
71B GLU 3.0 18.7 + - - -
177B TYR* 3.6 13.2 - - - +
238B TRP* 4.0 16.2 - - + -
250B TYR* 4.2 17.7 - - + -
266B MET* 3.9 8.7 - - - +
273B PRO* 4.1 13.0 - - + -
276B VAL* 3.3 27.9 - - + +
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Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP 3.9 6.3 - - - -
42B HIS* 3.7 17.5 - + - -
45B ALA* 3.7 24.6 - - + +
58B ALA 3.5 19.5 - - - +
59B ALA* 4.2 7.9 - - + -
64B ALA 2.9 20.5 + - - +
65B PHE 4.0 3.6 - - - +
67B PRO* 1.3 80.0 - - - +
69B HIS* 1.3 91.2 + + - +
71B GLU 3.2 2.1 + - - -
72B TYR* 2.8 70.6 + + - +
266B MET* 3.8 19.2 - - + -
267B TYR 2.9 28.3 + - - -
268B PRO* 3.9 3.6 - - + -
269B TRP* 3.2 28.1 - + - -
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Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 3.3 9.9 + - - -
59B ALA* 4.2 9.4 - - + -
60B HIS* 3.6 18.2 - + - -
65B PHE* 2.7 35.9 + + + +
66B LEU* 3.7 3.1 - - - +
68B TRP* 1.3 101.2 - + - +
70B ARG* 1.3 58.5 + - - +
72B TYR* 3.6 5.3 - + - +
73B LEU* 2.9 37.1 + - + +
227B PHE* 4.1 8.7 - + - -
231B HIS* 3.0 39.9 - + + +
234B VAL* 6.3 0.4 - - + -
235B ASP* 6.1 0.4 - - - -
401B CU 2.9 25.0 - - - -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU 2.9 18.3 + - - +
67B PRO* 3.2 13.9 - - + +
68B TRP 3.0 0.2 - - - -
69B HIS* 1.3 77.3 - - - +
71B GLU* 1.3 58.7 + - - +
72B TYR 3.1 0.9 + - - -
73B LEU* 3.2 6.2 + - - +
74B LEU* 2.7 28.0 + - - +
235B ASP* 2.6 37.0 + - + +
238B TRP* 2.7 38.0 + - + -
239B ALA* 4.5 2.2 - - - +
242B GLN* 1.8 40.0 + - - +
276B VAL* 1.9 44.2 + - + -
277B MET* 3.7 5.5 + - - +
278B ASN 3.9 1.9 - - - +
279B HIS* 4.3 18.9 - - - +
282B LEU* 4.6 7.9 - - - -
284B TYR* 3.6 15.6 + - - -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO 3.0 11.8 + - - +
68B TRP 3.6 2.2 - - - +
70B ARG* 1.3 72.6 - - - +
72B TYR* 1.3 51.0 + - - +
74B LEU* 3.5 19.7 - - + +
75B ARG* 1.9 84.2 + - + +
78B ARG* 5.8 0.5 + - - -
266B MET* 5.0 2.5 - - + -
269B TRP* 4.4 6.7 - - + -
271B THR* 1.8 56.5 + - + +
276B VAL* 3.5 18.1 - - + +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 1.9 54.5 + + - +
41B TRP* 4.0 9.0 - - + -
42B HIS* 3.2 18.8 - - + +
68B TRP* 2.8 58.0 + + + +
69B HIS* 3.6 7.6 - + - +
71B GLU* 1.3 78.7 - - - +
73B LEU* 1.3 69.4 + - + +
75B ARG* 4.1 2.9 - - - +
76B PHE* 3.2 22.7 + - - +
222B PRO* 3.9 4.5 - - - +
227B PHE* 4.2 17.5 - + - -
228B PHE* 3.7 28.5 - + - -
269B TRP* 3.8 12.3 - + + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 4.0 16.4 - - - +
69B HIS 2.9 23.7 + - - +
70B ARG 3.5 2.9 - - - +
72B TYR* 1.3 83.4 - - + +
74B LEU* 1.3 66.6 + - - +
76B PHE* 2.8 16.8 + - - +
77B GLU* 2.9 16.8 + - - +
89B LEU* 4.3 11.9 - - + +
227B PHE* 5.4 0.9 - - + -
228B PHE* 4.0 32.3 - - + +
231B HIS* 2.8 50.7 - - + +
232B ALA* 3.7 9.0 - - + +
235B ASP* 4.0 13.9 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 5.4 4.5 - - - +
8B ARG* 4.8 3.6 - - - +
70B ARG 2.7 21.9 + - - +
71B GLU* 3.5 27.6 - - + +
73B LEU* 1.3 75.1 - - - +
75B ARG* 1.3 58.3 + - - +
77B GLU* 3.1 28.1 + - + +
78B ARG* 3.7 44.4 + - - +
276B VAL* 4.8 0.4 - - + -
282B LEU* 3.7 52.0 - - + +
284B TYR* 5.0 10.7 - - + +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 4.4 15.4 + - - -
38B TYR* 1.7 27.8 + - - +
41B TRP* 4.2 15.3 - - + -
71B GLU* 1.9 84.3 + - + +
72B TYR* 4.0 3.4 - - - +
74B LEU* 1.3 72.2 - - + +
76B PHE* 1.3 50.7 - - - +
78B ARG* 4.8 16.0 - - - +
79B ASP* 3.3 16.0 - - - +
269B TRP* 3.3 44.8 - - - +
271B THR* 3.8 3.2 + - - -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 6.1 0.7 - + - -
26B VAL* 4.8 11.4 - - + -
29B LEU* 4.2 25.1 - - + -
35B TYR* 3.9 21.1 - + - -
38B TYR* 2.9 24.9 - + + -
72B TYR 3.2 17.8 + - - +
73B LEU 2.8 8.0 + - - +
75B ARG* 1.3 78.0 - - - +
77B GLU* 1.3 62.5 + - - +
79B ASP* 4.0 3.0 - - - +
80B LEU* 3.2 24.8 + - + +
89B LEU* 4.9 9.6 - - + -
228B PHE* 2.3 69.3 - + + -
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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
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6B ARG* 2.8 37.5 - - - +
8B ARG* 2.6 36.3 + - - -
73B LEU 2.9 8.2 + - - +
74B LEU* 3.3 13.6 - - + +
76B PHE* 1.3 75.2 - - - +
78B ARG* 1.3 57.2 + - + +
80B LEU* 2.2 56.0 + - + +
81B GLN* 2.7 16.8 + - - +
88B THR* 3.5 3.5 - - - -
89B LEU* 3.4 27.8 + - + +
284B TYR* 3.3 2.6 - - - -
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Residues in contact with ARG 78 (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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6B ARG* 4.8 14.8 - - - +
71B GLU* 5.8 0.8 + - - -
74B LEU* 3.7 50.1 + - - +
75B ARG* 4.8 11.3 - - - +
77B GLU* 1.3 76.1 - - - +
79B ASP* 1.3 59.7 + - - +
80B LEU 2.7 0.5 + - - -
81B GLN* 2.3 37.4 + - + -
82B SER* 2.3 27.7 + - - +
282B LEU* 3.8 16.6 + - - +
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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
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29B LEU* 3.1 33.8 - - + +
34B ILE* 4.3 20.9 - - + +
37B ARG* 5.9 0.9 + - - -
38B TYR* 4.3 6.5 - - + +
75B ARG* 3.3 19.7 - - - +
76B PHE 4.0 8.2 + - - +
77B GLU 3.1 0.6 + - - -
78B ARG* 1.3 83.4 - - - +
80B LEU* 1.3 56.2 + - - +
82B SER* 4.1 11.2 - - - +
83B ILE* 3.4 16.1 - - - +
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Residues in contact with LEU 80 (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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22B PHE* 4.1 20.2 - - + -
25B THR* 3.8 22.5 - - + +
26B VAL* 4.4 13.9 - - + -
29B LEU* 4.5 3.1 - - + -
76B PHE* 3.2 22.4 + - + +
77B GLU* 2.2 61.3 + - + +
78B ARG 3.0 2.2 - - - -
79B ASP* 1.3 67.3 - - - +
81B GLN* 1.3 49.8 + - - +
82B SER 3.0 1.6 - - - -
83B ILE* 2.9 5.0 + - - +
84B ASN* 2.6 36.4 + - - +
87B VAL* 4.3 15.3 - - + +
88B THR 4.8 2.5 - - - -
89B LEU* 4.1 24.7 - - + +
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Residues in contact with GLN 81 (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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6B ARG* 4.1 22.8 + - - +
77B GLU* 2.7 23.8 + - - +
78B ARG* 2.3 30.5 + - + +
80B LEU* 1.3 71.1 - - - +
82B SER* 1.3 59.3 + - - +
83B ILE 3.2 0.2 - - - -
84B ASN 3.9 6.3 - - - -
85B PRO* 2.1 54.9 + - + +
86B GLU* 4.4 0.2 - - - +
87B VAL 3.4 17.8 + - - +
88B THR* 4.1 12.1 - - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 2.3 36.8 + - - +
79B ASP* 4.1 9.0 + - - -
81B GLN* 1.3 71.9 - - - +
83B ILE* 1.3 67.4 + - - +
85B PRO* 5.1 0.7 - - - -
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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