Contacts of the helix formed by residues 76 - 87 (chain B) in PDB entry 2YVL
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 TYR 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.7 20.2 - - + -
70B ARG* 3.8 23.0 + - - -
73B GLN* 3.2 31.8 + - - -
74B ILE* 3.7 25.5 - - + +
75B ILE* 1.3 74.3 - - - +
77B PRO* 1.3 64.9 - - + +
78B LYS* 3.2 11.0 - - + +
79B ASP* 2.9 24.4 + - - +
80B SER* 2.9 12.8 + - - -
237B THR* 3.6 35.0 - - + -
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Residues in contact with PRO 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.5 1.2 - - - -
61B GLU* 3.8 39.5 - - + +
64B ILE* 4.1 28.3 - - + -
65B LEU* 3.5 27.1 - - + -
76B TYR* 1.3 80.8 - - + +
78B LYS* 1.3 65.6 + - - +
80B SER* 3.2 11.8 - - - +
81B PHE* 2.9 44.8 + - + +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.7 4.4 - - - +
61B GLU* 5.3 0.4 + - - -
76B TYR* 4.3 7.1 - - + +
77B PRO* 1.3 78.4 - - - +
79B ASP* 1.3 77.0 + - - +
81B PHE* 5.0 0.7 - - - +
82B TYR* 4.2 7.3 + - - +
215B ILE* 2.8 48.6 + - + +
217B HIS* 3.6 58.0 + - + +
234B VAL* 4.6 14.4 - - + -
236B HIS* 5.8 0.4 - - - +
237B THR* 2.8 45.3 + - - +
238B ALA 5.6 0.2 + - - -
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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 ILE* 4.1 7.7 - - + +
76B TYR* 2.9 13.1 + - - +
78B LYS* 1.3 99.0 + - - +
80B SER* 1.3 58.3 + - - +
81B PHE 3.3 0.7 - - - -
82B TYR* 3.3 4.7 + - - +
83B ILE* 2.8 40.8 + - + +
189B LEU* 4.4 8.0 - - - +
215B ILE* 3.7 18.8 + - - +
237B THR* 2.5 31.5 + - - +
238B ALA 4.4 3.6 + - - +
240B LEU* 4.0 24.0 - - + +
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Residues in contact with SER 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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64B ILE* 5.0 0.3 - - - +
75B ILE* 3.9 10.2 + - - +
76B TYR 2.9 10.5 + - - -
77B PRO* 3.2 20.4 - - - +
79B ASP* 1.3 74.3 - - - +
81B PHE* 1.3 63.4 + - - +
83B ILE* 3.7 10.6 - - - +
84B ALA* 3.0 31.5 + - - +
104B ALA 4.7 0.9 + - - -
105B LEU* 3.7 25.1 - - - +
108B VAL* 3.4 23.2 - - - +
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE 3.9 14.9 - - - +
82A TYR* 3.7 34.8 - + + -
85A LEU* 3.6 43.2 - - + +
86A LYS* 3.6 22.2 - - - -
60B LEU* 3.9 13.9 - - + -
61B GLU* 3.9 27.6 - - + -
64B ILE* 4.4 2.0 - - + -
77B PRO* 2.9 38.4 + - + +
80B SER* 1.3 82.0 - - - +
82B TYR* 1.3 63.0 + - - +
85B LEU* 3.9 11.3 + - - +
108B VAL* 3.8 27.4 - - + -
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 2.6 31.3 + - - -
77A PRO 4.5 6.7 - - - -
78A LYS* 4.7 4.5 - - - +
81A PHE* 3.6 32.0 - + + -
82A TYR* 5.1 2.1 - - + +
217A HIS* 3.6 26.6 + + + +
219A HIS* 5.1 7.3 - - - -
78B LYS 4.2 5.0 + - - +
79B ASP 3.3 8.0 + - - +
81B PHE* 1.3 77.4 - - - +
83B ILE* 1.3 61.7 + - - +
85B LEU 3.4 1.6 + - - -
86B LYS* 2.8 63.3 + - + +
211B GLU* 5.2 0.2 + - - -
213B VAL* 4.4 13.1 - - + +
215B ILE* 3.7 26.9 - - + -
240B LEU* 4.6 1.8 - - + -
242B PHE* 3.9 18.6 - + - -
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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
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75B ILE* 4.2 9.9 - - + -
79B ASP* 2.8 42.7 + - + +
80B SER* 3.7 9.6 - - - +
82B TYR* 1.3 71.9 - - - +
84B ALA* 1.3 64.3 + - - +
86B LYS* 3.6 0.5 - - - +
87B LEU* 2.9 36.2 + - + +
105B LEU* 4.1 14.1 - - + -
109B LEU* 4.8 0.4 - - + -
163B PHE* 3.5 46.2 - - + -
240B LEU* 4.0 12.6 - - + -
242B PHE* 3.8 25.4 - - + -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.6 0.9 - - + -
80B SER 3.0 16.7 + - - +
81B PHE 4.3 2.9 - - - +
83B ILE* 1.3 80.7 - - - +
85B LEU* 1.3 61.3 + - - +
87B LEU 3.8 1.4 + - - -
89B LEU* 3.4 37.4 + - + +
108B VAL* 3.8 22.4 - - + +
109B LEU* 4.4 11.4 - - + -
112B VAL* 3.9 22.4 - - + +
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Residues in contact with LEU 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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59A THR* 5.6 0.3 - - - -
60A LEU* 4.2 26.1 + - + +
61A GLU 5.3 0.7 + - - -
81A PHE* 3.5 65.3 - - + +
84A ALA* 4.8 0.4 - - + -
85A LEU* 4.0 13.9 - - + -
108A VAL* 3.9 13.5 - - + -
111A GLU* 4.9 4.0 - - + -
112A VAL* 3.9 24.7 - - + -
81B PHE 3.9 6.6 + - - +
82B TYR 3.4 1.6 + - - +
83B ILE 3.3 0.2 - - - -
84B ALA* 1.3 76.2 - - - +
86B LYS* 1.3 62.0 + - - +
87B LEU 3.2 1.3 - - - -
88B ASN* 2.9 20.0 + - - +
89B LEU 4.4 15.9 - - - +
112B VAL* 4.4 7.6 - - + -
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Residues in contact with LYS 86 (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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18A LYS* 3.9 4.9 - - - +
59A THR* 4.3 17.8 + - - +
61A GLU* 2.8 33.1 + - + +
62A GLU* 5.1 1.2 + - - -
81A PHE* 3.5 6.4 - - + -
82B TYR* 2.8 49.8 + - + +
83B ILE* 3.6 4.9 - - - +
85B LEU* 1.3 73.4 - - - +
87B LEU* 1.3 56.8 + - - +
88B ASN* 3.0 12.5 + - - +
185B PRO* 4.8 2.8 - - - +
211B GLU* 2.7 36.8 + - - -
242B PHE* 3.7 40.6 - - + -
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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
----------------------------------------------------------
83B ILE* 2.9 38.2 + - + +
84B ALA 3.9 5.4 - - - +
85B LEU 3.2 0.4 - - - -
86B LYS* 1.3 72.5 - - - +
88B ASN* 1.3 68.8 + - - +
89B LEU* 3.3 20.9 + - + +
95B VAL* 4.5 5.4 - - + -
109B LEU* 4.5 5.2 - - + -
160B HIS 4.8 0.7 - - - +
161B ALA* 3.8 13.0 - - + +
162B ALA 3.7 17.7 - - - +
163B PHE* 4.1 11.9 - - + -
185B PRO* 3.7 28.8 - - + +
186B VAL* 3.8 7.0 - - - -
187B GLY* 3.6 26.2 - - - +
242B PHE* 4.2 11.7 - - + -
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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
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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