Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 1YH8
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 VAL 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.8 29.8 - - + -
60B THR* 3.1 23.3 + - + +
62B LEU* 4.0 22.2 - - + -
74B ILE* 4.1 34.3 - - + +
76B THR* 1.3 74.3 - - - +
78B GLU* 1.3 62.0 + - - +
79B HIS 3.4 2.5 - - - -
80B ILE* 3.3 5.2 - - - +
81B LEU* 3.0 50.6 + - + +
101B ILE* 4.0 6.5 - - + -
249B LEU* 4.9 0.4 - - + -
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Residues in contact with GLU 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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59B SER* 3.4 13.5 - - - -
60B THR* 3.0 24.1 + - - +
76B THR* 3.2 17.5 - - - +
77B VAL* 1.3 89.2 + - - +
79B HIS* 1.3 79.3 + - + +
81B LEU* 4.6 3.8 - - - -
82B SER* 3.0 30.0 + - - -
241B PHE 4.7 0.7 - - - +
242B ASP* 3.7 11.0 - - - +
245B GLY* 3.4 8.6 - - - -
246B ASP* 4.1 12.6 - - - +
265B HIS* 3.3 21.8 + - + -
802B PAM 2.9 22.2 - - - +
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Residues in contact with HIS 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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76B THR* 4.9 7.5 + - + +
77B VAL 3.4 0.8 - - - -
78B GLU* 1.3 80.2 - - + +
80B ILE* 1.3 65.8 + - - +
82B SER 3.5 0.2 + - - -
83B VAL* 3.2 28.1 + - - +
101B ILE* 6.2 1.6 - - + -
103B ILE* 3.7 22.9 + - + +
106B GLY 3.5 15.7 + - - -
107B SER 4.4 8.7 + - - +
111B PHE* 4.4 9.9 - - + -
191B THR* 3.1 21.3 - - - -
238B HIS* 3.1 2.1 + + - -
241B PHE* 3.4 25.7 - + + -
242B ASP* 3.3 9.9 - - - -
505B ZN 2.1 36.8 - - - -
802B PAM 3.1 6.5 + - - -
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Residues in contact with ILE 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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26B LEU* 4.5 10.8 - - + -
28B ILE* 5.1 7.4 - - + -
39B PHE* 4.3 20.2 - - + -
77B VAL* 3.3 18.8 - - - +
79B HIS* 1.3 75.4 - - - +
81B LEU* 1.3 65.7 + - + +
83B VAL* 3.4 1.9 + - + +
84B LEU* 3.0 45.0 + - + +
94B ILE* 4.5 8.5 - - + -
101B ILE* 4.2 17.6 - - + +
111B PHE* 3.6 45.4 - - + -
115B ILE* 4.1 20.6 - - + -
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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
----------------------------------------------------------
37B ILE* 4.0 15.3 - - + -
39B PHE* 3.8 21.8 - - + -
48B ALA* 3.9 20.9 - - + -
77B VAL* 3.0 48.0 + - + +
78B GLU* 4.1 2.0 - - - +
80B ILE* 1.3 77.6 - - - +
82B SER* 1.3 55.0 + - - +
84B LEU* 3.2 8.1 + - + -
85B HIS* 2.7 35.5 + - - +
94B ILE* 4.6 0.2 - - + -
245B GLY* 3.9 18.2 - - - +
248B TYR* 3.4 14.9 - - + -
249B LEU* 3.8 24.7 - - + +
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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 GLU 3.0 19.6 + - - -
79B HIS 3.6 5.6 - - - -
80B ILE 3.3 0.2 - - - -
81B LEU* 1.3 77.3 - - - +
83B VAL* 1.3 57.4 + - - +
85B HIS* 3.0 5.3 + - - +
86B LEU* 2.8 35.7 + - - +
241B PHE* 2.7 48.4 + - - -
244B ILE* 3.6 8.7 - - - +
245B GLY* 3.4 13.3 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS 3.2 15.1 + - - +
80B ILE 3.7 6.5 - - - +
81B LEU 3.3 0.2 - - - -
82B SER* 1.3 76.7 - - - +
84B LEU* 1.3 61.5 + - - +
86B LEU* 3.3 8.6 + - - +
87B LEU* 3.0 36.8 + - + +
108B GLY* 3.6 22.2 - - - +
111B PHE* 3.9 15.0 - - + -
112B TYR* 3.6 34.3 - - + +
115B ILE* 4.1 9.2 - - + -
187B VAL* 5.1 1.8 - - + -
241B PHE* 3.7 15.7 - - + -
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Residues in contact with LEU 84 (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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28B ILE* 5.6 5.4 - - + -
37B ILE* 3.9 17.7 - - + -
80B ILE* 3.0 30.0 + - + +
81B LEU* 3.2 10.1 + - + +
83B VAL* 1.3 76.2 - - - +
85B HIS* 1.3 58.3 + - - +
88B GLU* 3.0 21.8 + - - -
89B ILE* 3.0 43.6 + - + +
92B VAL* 4.2 10.5 - - + -
94B ILE* 3.7 31.4 - - + -
115B ILE* 3.7 26.2 - - + -
248B TYR* 3.8 12.3 - - + -
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Residues in contact with HIS 85 (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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81B LEU 2.7 20.8 + - - +
82B SER 3.3 5.2 - - - +
84B LEU* 1.3 74.8 - - - +
86B LEU* 1.3 63.4 + - - +
88B GLU* 3.2 15.4 + - - +
153B LEU* 3.9 21.3 - - + +
244B ILE* 2.8 30.8 + - + +
247B LEU* 4.1 6.1 - - + -
248B TYR* 3.6 32.2 - + + +
253B PRO* 3.5 17.2 - - + +
254B VAL* 2.9 46.2 + - + +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 2.8 27.8 + - - +
83B VAL* 3.7 6.1 - - - +
85B HIS* 1.3 79.2 - - - +
87B LEU* 1.3 61.7 + - - +
88B GLU* 3.1 4.7 + - - +
112B TYR* 4.9 4.5 - - + -
153B LEU* 5.3 3.8 - - + -
175B PHE* 3.6 34.5 - - + -
183B GLU* 4.2 25.3 - - + +
186B ILE* 4.1 15.0 - - + -
187B VAL* 3.9 28.5 - - + -
241B PHE* 4.2 4.7 - - + -
244B ILE* 3.9 22.4 - - + -
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Residues in contact with LEU 87 (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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5B LYS* 3.5 15.4 - - - +
83B VAL* 3.0 26.2 + - + +
86B LEU* 1.3 74.6 - - - +
88B GLU* 1.3 70.0 + - - +
89B ILE* 3.4 15.4 + - + +
112B TYR* 3.2 40.6 - - + +
115B ILE* 3.4 37.5 - - + +
116B ARG* 3.5 27.4 - - + +
120B ILE* 4.4 11.3 - - + +
183B GLU* 5.8 1.1 - - + -
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Residues in contact with GLU 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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2B GLY* 4.2 3.6 - - - -
5B LYS* 3.3 32.4 + - - +
84B LEU 3.0 7.5 + - - -
85B HIS 3.2 10.3 + - - +
86B LEU 3.1 7.7 - - - +
87B LEU* 1.3 81.5 - - - +
89B ILE* 1.3 63.8 + - - +
90B THR* 3.4 13.2 + - - +
127B ILE* 3.1 18.8 - - + +
129B TYR* 3.1 32.5 + - - -
180B GLU* 5.1 1.7 - - - +
248B TYR* 4.7 0.4 - - - -
253B PRO* 4.2 16.6 - - + -
255B LYS* 3.9 10.0 + - - -
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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
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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