Contacts of the helix formed by residues 62 - 80 (chain B) in PDB entry 4R0C
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 ASP 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B HIS* 5.6 1.2 - - - +
59B SER* 2.8 41.7 + - - +
61B LEU* 1.3 80.4 - - - +
63B ALA* 1.3 64.6 + - - +
64B ASP* 3.6 19.3 + - - +
65B GLY 3.0 10.0 + - - -
66B LEU* 2.8 27.2 + - - +
353B TYR* 5.2 0.2 + - - -
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Residues in contact with ALA 63 (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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275A ASP 5.5 3.6 - - - +
277A PRO* 3.8 24.2 - - + +
62B ASP* 1.3 77.6 + - - +
64B ASP* 1.3 64.9 - - - +
66B LEU* 4.6 1.1 - - - -
67B ARG* 3.1 42.1 + - - +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 3.2 14.5 + - - +
63B ALA* 1.3 80.1 - - - +
65B GLY* 1.3 59.5 + - - +
67B ARG* 3.1 24.4 + - - +
68B TYR* 2.9 27.5 + - - +
353B TYR* 3.5 12.1 + - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER 3.7 12.3 - - - -
60B LEU* 3.3 17.3 - - - +
62B ASP* 3.0 10.8 + - - -
64B ASP* 1.3 77.9 - - - +
66B LEU* 1.3 53.9 + - - +
68B TYR* 2.9 8.0 + - - +
69B LEU* 2.7 35.2 + - - +
353B TYR* 3.7 14.1 + - - -
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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
----------------------------------------------------------
270A LEU* 3.6 26.2 - - + -
277A PRO* 4.0 18.6 - - + -
278A LEU* 4.6 1.1 - - + -
60B LEU 3.3 12.7 + - - +
61B LEU* 3.6 34.1 - - + +
62B ASP 2.8 17.1 + - - +
63B ALA* 3.9 4.0 - - - +
65B GLY* 1.3 74.1 - - - +
67B ARG* 1.3 63.9 + - - +
69B LEU* 3.1 12.1 + - + +
70B PHE* 3.0 42.3 + - + -
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASP 5.0 2.8 + - - -
276A ALA 4.5 3.2 + - - -
277A PRO* 2.9 39.6 + - - +
278A LEU* 4.3 9.1 - - - +
279A ARG 4.1 5.1 + - - -
281A PRO* 4.1 42.9 - - - +
290A PRO* 4.0 16.6 - - + -
63B ALA* 3.1 31.8 + - - +
64B ASP* 3.1 32.1 + - - +
66B LEU* 1.3 79.2 - - - +
68B TYR* 1.3 58.9 + - - +
70B PHE 3.4 0.7 + - - -
71B THR* 2.9 36.0 + - + +
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.2 8.1 - - + -
64B ASP 2.9 15.0 + - - +
65B GLY 2.9 9.5 + - - +
67B ARG* 1.3 78.2 - - - +
69B LEU* 1.3 60.9 + - + +
71B THR* 3.8 4.0 - - - -
72B THR* 2.6 64.3 + - + +
76B ASN* 4.1 3.6 + - - -
349B ALA* 2.9 37.1 + - - +
350B TRP* 3.8 21.1 - + - -
353B TYR* 3.4 58.6 - + + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.0 20.2 - - + -
60B LEU* 3.5 32.3 - - + +
61B LEU* 4.7 1.6 - - + -
65B GLY 2.7 9.0 + - - +
66B LEU* 3.3 22.4 - - + +
68B TYR* 1.3 84.5 - - + +
70B PHE* 1.3 68.6 + - + +
71B THR 3.5 0.2 + - - -
72B THR* 4.0 1.9 + - - -
73B LEU* 3.5 28.4 + - - +
350B TRP* 3.5 50.8 + - + +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 5.4 2.7 - - + -
270A LEU* 3.6 26.9 - - + -
278A LEU* 3.7 37.7 - - + -
290A PRO* 4.2 14.6 - - + +
294A GLY* 5.1 6.4 - - - -
298A ILE* 4.3 24.0 - - + -
301A LEU* 5.1 16.4 - - + -
66B LEU* 3.0 40.5 + - + +
67B ARG 4.3 0.9 - - - +
69B LEU* 1.3 83.2 - - + +
71B THR* 1.3 63.1 + - - +
72B THR 3.6 0.2 - - - -
73B LEU* 5.0 3.4 - - - -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PRO* 3.8 30.7 - - + -
67B ARG* 2.9 22.8 + - + +
68B TYR* 3.4 6.6 + - - -
70B PHE* 1.3 83.6 - - - +
72B THR* 1.3 70.6 + - - +
73B LEU 3.8 1.1 - - - -
75B GLY 5.5 1.0 + - - -
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Residues in contact with THR 72 (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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68B TYR* 2.6 51.8 + - + +
69B LEU* 4.0 2.3 + - - -
71B THR* 1.3 91.7 - - - +
73B LEU* 1.3 57.5 + - - +
74B VAL 3.5 1.8 - - - -
75B GLY* 3.1 5.9 + - - +
76B ASN* 2.8 57.3 + - - -
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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
----------------------------------------------------------
88A VAL* 4.1 12.3 - - + -
297A VAL* 4.0 27.1 - - + -
301A LEU* 6.1 5.4 - - + -
806A LMT 4.7 7.4 - - + -
69B LEU 3.5 18.0 + - - +
70B PHE* 5.0 2.9 - - - -
71B THR 3.8 1.4 - - - -
72B THR* 1.3 76.2 - - - +
74B VAL* 1.3 65.8 + - + +
76B ASN* 3.5 2.6 - - - +
77B PHE* 3.9 0.9 - - - +
342B PHE* 4.0 14.9 - - + -
346B GLN* 2.6 57.2 + - + +
350B TRP* 4.4 15.7 - - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 3.5 8.5 - - - +
85A VAL* 3.5 43.5 - - + +
88A VAL* 4.1 20.4 - - + -
297A VAL* 4.1 19.1 - - + -
72B THR 3.5 0.4 - - - -
73B LEU* 1.3 80.3 - - + +
75B GLY* 1.3 59.5 + - - +
77B PHE* 3.0 18.2 + - - +
78B THR* 3.0 24.2 + - + -
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Residues in contact with GLY 75 (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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71B THR 5.5 1.0 + - - -
72B THR* 3.1 9.3 + - - +
74B VAL* 1.3 75.0 - - - +
76B ASN* 1.3 66.2 + - - +
77B PHE 3.0 1.3 - - - -
78B THR* 3.7 8.7 + - - -
79B GLY* 3.1 23.0 + - - -
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Residues in contact with ASN 76 (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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68B TYR* 4.1 4.9 + - - -
69B LEU 5.6 0.2 + - - -
72B THR* 2.8 50.9 + - - +
73B LEU* 4.0 0.6 - - - +
75B GLY* 1.3 71.6 - - - +
77B PHE* 1.3 56.6 + - - +
79B GLY 4.1 0.3 - - - -
80B PHE* 3.2 28.4 + - - +
345B ALA* 3.6 9.2 - - - +
346B GLN* 2.6 34.4 + - - +
349B ALA* 3.6 30.6 - - + +
350B TRP* 4.0 8.5 - - - +
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Residues in contact with PHE 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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84A GLY 4.9 1.1 - - - -
87A LEU* 4.0 30.7 - - + -
88A VAL* 3.9 18.6 - - + -
91A LEU* 6.4 0.2 - - + -
331A MET* 5.8 3.6 - - - -
73B LEU 3.9 4.9 - - - +
74B VAL* 3.0 11.0 + - - +
76B ASN* 1.3 75.9 - - - +
78B THR* 1.3 74.7 + - + +
79B GLY 3.2 1.3 - - - -
80B PHE* 3.1 17.9 + - + +
83B LEU* 3.5 35.9 - - + +
338B LEU* 3.6 26.5 - - + -
341B MET* 4.1 5.2 - - + -
342B PHE* 3.4 54.5 - + + -
345B ALA* 4.2 5.2 - - + -
346B GLN* 4.0 1.6 - - - +
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Residues in contact with THR 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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78A THR* 3.2 49.9 + - - +
79A GLY* 5.3 2.1 - - - -
83A LEU* 5.5 3.1 - - + -
84A GLY* 3.5 32.3 - - - +
74B VAL* 3.0 22.6 + - + +
75B GLY* 3.7 10.6 + - - -
77B PHE* 1.3 77.8 - - + +
79B GLY* 1.3 61.8 + - - +
80B PHE 3.7 3.5 + - - +
83B LEU* 4.5 11.3 - - - +
84B GLY 5.0 0.2 + - - -
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Residues in contact with GLY 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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78A THR* 5.4 2.2 - - - -
75B GLY 3.1 12.5 + - - -
76B ASN 4.1 0.7 - - - -
78B THR* 1.3 81.1 + - - +
80B PHE* 1.3 66.1 + - - +
81B ALA* 3.0 6.2 + - - -
189B GLU* 4.0 3.9 - - - +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN 3.2 13.1 + - - +
77B PHE* 3.1 16.9 + - + +
78B THR 4.3 0.9 - - - +
79B GLY* 1.3 74.7 - - - +
81B ALA* 1.3 66.0 + - - +
82B PRO* 3.4 21.1 - - + -
83B LEU* 3.0 20.6 + - + +
84B GLY 4.2 2.6 + - - -
186B LEU* 3.8 20.6 - - + -
189B GLU* 3.4 39.3 - - + -
341B MET* 3.7 25.1 - - + -
344B ALA* 3.9 9.0 - - + -
345B ALA* 3.4 44.2 - - + -
348B VAL* 4.0 13.0 - - + -
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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