Contacts of the helix formed by residues 63 - 76 (chain B) in PDB entry 4Y2H
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 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A TYR* 4.0 1.1 - - - -
59B GLU 3.1 13.7 + - - +
60B MET 3.4 11.7 - - - +
61B ILE 3.2 1.0 - - - -
62B ALA* 1.3 73.0 - - - +
64B ARG* 1.3 58.6 + - - +
65B VAL* 3.4 10.0 + - - +
66B ARG* 3.0 26.1 + - + +
67B THR* 2.9 31.5 + - - -
315B ALA 4.5 1.0 - - - +
316B THR* 3.5 10.5 - - - -
317B HIS* 2.8 49.2 + - + +
318B TRP* 4.1 0.5 - - - -
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Residues in contact with ARG 64 (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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214A HIS* 3.5 51.1 + - - +
215A TYR* 3.2 20.0 + - - +
61B ILE 5.0 0.2 - - - +
62B ALA* 2.9 15.6 + - - +
63B ASP* 1.3 70.2 + - - +
65B VAL* 1.3 62.6 + - + +
68B ASP* 2.8 42.2 + - - +
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Residues in contact with VAL 65 (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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63B ASP* 3.4 6.9 - - - +
64B ARG* 1.3 77.7 - - + +
66B ARG* 1.3 63.8 + - - +
68B ASP* 4.5 1.9 - - - +
69B ALA* 3.1 27.5 + - + +
307B LEU* 3.7 19.3 - - + -
308B SER 4.5 5.6 - - - +
314B PRO* 3.8 26.2 - - + +
315B ALA 3.7 16.8 - - - +
316B THR* 3.7 15.9 - - + -
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Residues in contact with ARG 66 (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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60B MET* 2.9 41.3 + - - +
61B ILE* 3.9 6.7 - - - +
63B ASP* 3.0 25.2 + - - +
65B VAL* 1.3 80.3 - - - +
67B THR* 1.3 79.8 + - - +
69B ALA* 3.3 1.6 + - - +
70B TYR* 3.2 29.1 + - + -
95B ILE* 4.8 1.8 - - - +
96B LEU* 5.2 2.1 - - - +
155B GLU* 2.8 47.4 + - + +
307B LEU* 4.1 13.7 - - + -
316B THR* 5.2 0.4 - - - +
317B HIS* 3.8 13.7 - - - -
318B TRP* 3.4 27.8 - - + -
401B SAH 2.8 40.0 + - - -
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Residues in contact with THR 67 (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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215A TYR* 3.5 35.9 - - + -
60B MET 3.0 17.3 + - - -
61B ILE* 3.7 7.5 - - - +
63B ASP 2.9 13.3 + - - -
66B ARG* 1.3 93.7 + - - +
68B ASP* 1.3 58.8 + - - +
70B TYR* 3.4 5.8 + - - +
71B ARG* 3.1 26.0 + - - +
95B ILE* 4.4 10.3 - - + -
96B LEU* 5.2 2.0 - - + -
99B PHE* 3.8 20.9 - - + -
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Residues in contact with ASP 68 (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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214A HIS* 2.9 25.5 + - - -
215A TYR* 3.3 19.5 - - - -
64B ARG* 2.8 29.2 + - - +
65B VAL* 4.5 1.6 - - - +
67B THR* 1.3 70.5 - - - +
69B ALA* 1.3 59.3 + - - +
71B ARG* 3.3 26.2 + - - +
72B LEU* 2.9 45.2 + - + +
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Residues in contact with ALA 69 (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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65B VAL* 3.1 20.8 + - + +
66B ARG 3.3 4.2 + - - +
68B ASP* 1.3 78.6 - - - +
70B TYR* 1.3 56.4 + - - +
72B LEU* 4.8 0.2 - - - -
73B GLY* 2.8 27.0 + - - -
296B PHE* 3.9 4.9 - - + -
305B LEU* 3.4 29.0 - - + +
306B VAL 5.3 0.9 - - - +
307B LEU* 3.9 27.1 - - + -
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Residues in contact with TYR 70 (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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66B ARG* 3.2 20.8 + - + +
67B THR* 3.8 6.5 - - - +
69B ALA* 1.3 75.7 - - - +
71B ARG* 1.3 55.6 + - - +
73B GLY* 3.2 0.5 + - - -
74B ILE* 2.7 43.3 + - + +
96B LEU* 3.7 36.1 - - + -
153B VAL* 4.1 13.0 - - + -
154B SER 2.7 33.8 + - - -
155B GLU* 3.2 29.6 - - + -
157B MET* 3.5 12.2 - - + +
186B PRO* 3.3 12.8 - - + +
296B PHE* 3.6 34.4 - + - -
307B LEU* 4.0 17.9 - - + -
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Residues in contact with ARG 71 (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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214A HIS* 3.0 31.6 + - - -
215A TYR* 3.6 24.5 + - - +
216A GLY* 4.2 2.2 - - - +
67B THR 3.1 16.9 + - - +
68B ASP* 3.3 27.7 + - - +
70B TYR* 1.3 76.2 - - - +
72B LEU* 1.3 61.1 + - - +
74B ILE* 3.3 3.1 + - - +
75B LEU* 2.7 44.6 + - + +
99B PHE* 3.7 39.4 - - + +
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Residues in contact with LEU 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 ASP* 2.9 37.1 + - + +
71B ARG* 1.3 82.0 - - - +
73B GLY* 1.3 61.3 + - - +
75B LEU* 3.9 9.7 - - + +
76B ARG* 2.9 47.5 + - - +
305B LEU* 3.5 24.0 - - + -
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Residues in contact with GLY 73 (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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69B ALA 2.8 23.5 + - - -
70B TYR 3.2 0.9 + - - -
72B LEU* 1.3 74.7 - - - +
74B ILE* 1.3 57.3 + - - +
76B ARG* 3.7 3.9 + - - +
77B ASN* 2.6 32.6 + - - -
185B LEU* 4.3 2.1 - - - +
296B PHE* 4.0 28.5 - - - -
305B LEU* 3.9 6.2 - - - +
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Residues in contact with ILE 74 (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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70B TYR* 2.7 33.6 + - + +
71B ARG* 3.5 3.6 - - - +
73B GLY* 1.3 70.6 - - - +
75B LEU* 1.3 56.4 + - + +
77B ASN* 2.8 35.2 + - - +
78B TRP* 3.6 0.7 + - - -
81B LEU* 3.8 21.8 - - + +
96B LEU* 4.0 12.6 - - + +
99B PHE* 3.7 36.3 - - + +
100B CYS* 4.0 9.2 - - - -
103B ALA* 3.8 15.0 - - + -
153B VAL* 4.1 21.3 - - + -
185B LEU* 4.2 19.5 - - + -
296B PHE* 5.5 0.7 - - + -
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Residues in contact with LEU 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 ARG* 2.7 29.1 + - + +
72B LEU* 3.9 11.7 - - + +
74B ILE* 1.3 73.7 - - - +
76B ARG* 1.3 58.0 + - - +
77B ASN 3.1 1.0 + - - -
78B TRP* 3.1 38.6 + - + +
99B PHE 5.6 1.1 - - - +
102B GLN* 5.2 3.4 - - + +
103B ALA* 4.3 24.7 - - + +
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Residues in contact with ARG 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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72B LEU* 2.9 32.0 + - - +
73B GLY* 3.8 8.5 - - - +
74B ILE 3.0 0.4 + - - -
75B LEU* 1.3 76.1 - - - +
77B ASN* 1.3 62.0 + - - +
78B TRP* 3.5 3.7 + - - -
79B ALA* 5.4 0.7 + - - +
298B GLY* 4.8 4.0 - - - -
299B GLY* 3.5 13.4 + - - +
301B SER* 3.1 38.4 + - - +
302B GLU* 3.4 34.6 + - + +
303B LYS 2.8 33.8 + - - +
304B PRO 3.9 11.5 + - - -
305B LEU* 3.7 29.6 - - + +
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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