Contacts of the helix formed by residues 76 - 87 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LEU* 3.5 23.6 - - + -
70D ARG* 3.7 20.4 + - - -
73D GLN* 3.3 29.2 + - - -
74D ILE* 3.6 27.0 - - + +
75D ILE* 1.3 75.1 - - - +
77D PRO* 1.3 63.3 - - + +
78D LYS* 3.1 13.5 - - + +
79D ASP* 2.8 29.8 + - - +
80D SER* 3.0 10.2 + - - -
237D THR* 3.6 34.5 - - + -
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Residues in contact with PRO 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 4.8 0.7 - - - -
61D GLU* 3.7 40.8 - - + +
64D ILE* 4.2 22.4 - - + -
65D LEU* 3.8 24.0 - - + -
76D TYR* 1.3 86.0 - - + +
78D LYS* 1.3 62.5 + - - +
80D SER* 3.1 12.5 - - - +
81D PHE* 2.9 50.9 + - + +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 4.7 4.8 - - - +
61D GLU* 5.3 0.2 + - - -
76D TYR* 4.3 8.5 - - + +
77D PRO* 1.3 78.8 - - - +
79D ASP* 1.3 77.2 + - - +
81D PHE* 5.0 0.7 - - - +
82D TYR* 4.3 6.2 + - - +
215D ILE* 2.8 49.6 + - + +
216D LEU* 4.6 0.9 - - - +
217D HIS* 3.7 56.7 - - + +
234D VAL* 4.6 14.1 - - + +
236D HIS* 5.7 0.4 - - - +
237D THR* 2.8 47.1 + - - +
238D ALA 5.4 1.0 + - - -
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ILE* 4.1 7.2 - - + +
76D TYR 2.8 17.2 + - - +
78D LYS* 1.3 93.9 + - - +
80D SER* 1.3 58.7 + - - +
81D PHE 3.3 0.4 - - - -
82D TYR* 3.3 5.9 + - - +
83D ILE* 2.9 44.6 + - + +
189D LEU* 4.5 6.1 - - + +
215D ILE* 3.8 19.1 + - - +
237D THR* 2.5 31.1 + - - +
238D ALA 4.3 3.7 + - - +
240D LEU* 4.0 19.0 - - + +
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 5.2 0.3 - - - +
75D ILE* 3.8 13.2 + - - -
76D TYR 3.0 4.5 + - - -
77D PRO* 3.1 23.2 - - - +
79D ASP* 1.3 74.9 - - - +
81D PHE* 1.3 60.0 + - - +
83D ILE* 3.8 9.1 - - - +
84D ALA* 3.0 32.2 + - - +
104D ALA 4.6 0.7 + - - -
105D LEU* 3.6 27.1 - - - +
108D VAL* 3.4 25.0 - - - +
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Residues in contact with PHE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PHE 3.8 15.5 - - - +
82C TYR* 3.6 35.4 - + + -
85C LEU* 3.6 45.1 - - + +
86C LYS* 3.5 23.1 - - - -
60D LEU* 4.0 13.9 - - + -
61D GLU* 3.8 25.8 - - + -
64D ILE* 4.8 0.7 - - + -
77D PRO* 2.9 38.0 + - + +
78D LYS 5.0 0.2 - - - +
80D SER* 1.3 80.3 - - - +
82D TYR* 1.3 62.2 + - - +
85D LEU* 3.9 12.0 + - - +
108D VAL* 3.9 24.7 - - + -
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 2.6 33.0 + - - -
77C PRO 4.5 5.4 - - - -
78C LYS* 4.8 4.3 - - - +
81C PHE* 3.7 31.5 - + + +
82C TYR* 5.2 1.5 - - + +
217C HIS* 3.6 27.6 + + + -
219C HIS* 5.0 8.3 - - - -
78D LYS 4.3 4.3 + - - +
79D ASP 3.3 8.3 + - - +
81D PHE* 1.3 77.3 - - - +
83D ILE* 1.3 55.3 + - - +
85D LEU* 3.3 2.8 + - - -
86D LYS* 2.8 54.3 + - + +
213D VAL* 4.2 13.1 - - + +
215D ILE* 3.6 26.9 - - + -
240D LEU* 4.4 2.5 - - + -
242D PHE* 3.8 28.7 - + - -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ILE* 4.3 9.6 - - + -
79D ASP* 2.9 40.8 + - + +
80D SER* 3.5 9.6 + - - +
82D TYR* 1.3 71.8 - - - +
84D ALA* 1.3 60.0 + - - +
86D LYS* 3.7 0.3 - - - +
87D LEU* 2.8 42.9 + - + +
105D LEU* 4.0 14.6 - - + -
109D LEU* 4.9 0.7 - - + -
163D PHE* 3.5 47.1 - - + -
189D LEU* 4.8 0.2 - - + -
240D LEU* 4.1 12.6 - - + -
242D PHE* 3.9 25.8 - - + -
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 4.7 0.7 - - + -
80D SER 3.0 17.5 + - - +
81D PHE 4.4 3.4 - - - +
82D TYR 3.4 0.2 - - - -
83D ILE* 1.3 81.2 - - - +
85D LEU* 1.3 61.9 + - - +
87D LEU* 3.7 1.6 + - - -
89D LEU* 3.3 33.3 + - + +
108D VAL* 3.8 21.8 - - + +
109D LEU* 4.3 18.2 - - + -
112D VAL* 4.0 20.4 - - + -
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C THR* 5.7 0.3 - - - -
60C LEU* 4.8 16.3 + - + +
61C GLU 5.3 0.7 + - - -
81C PHE* 3.5 65.6 - - + +
84C ALA* 4.6 0.7 - - + -
85C LEU* 3.9 18.2 - - + -
108C VAL* 4.0 15.7 - - + -
111C GLU* 5.6 3.1 - - + -
112C VAL* 4.0 19.1 - - + -
81D PHE 3.9 3.9 + - - +
82D TYR 3.3 1.4 + - - -
83D ILE 3.3 0.2 - - - -
84D ALA* 1.3 77.2 - - - +
86D LYS* 1.3 61.8 + - - +
87D LEU 3.3 0.4 - - - -
88D ASN* 3.1 18.3 + - - +
89D LEU 4.2 8.7 - - - +
112D VAL* 3.7 28.0 - - + -
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 4.0 4.8 - - - +
59C THR* 4.3 17.4 + - - +
61C GLU* 2.7 34.3 + - + +
62C GLU* 4.9 2.2 + - - -
81C PHE* 3.6 6.2 - - + -
82D TYR* 2.8 49.2 + - + +
83D ILE 3.7 3.4 - - - +
85D LEU* 1.3 73.3 - - - +
87D LEU* 1.3 55.9 + - - +
88D ASN* 2.9 13.4 + - - +
185D PRO* 4.7 3.1 - - - +
211D GLU* 2.7 37.2 + - - -
242D PHE* 3.7 42.2 - - + -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ILE* 2.8 38.3 + - + +
84D ALA 3.8 0.4 - - - +
85D LEU 3.3 0.2 - - - -
86D LYS* 1.3 73.0 - - - +
88D ASN* 1.3 68.4 + - - +
89D LEU* 3.2 27.6 + - + +
93D LYS* 5.7 0.3 - - - +
95D VAL* 4.6 1.3 - - + -
109D LEU* 4.3 7.0 - - + -
160D HIS 4.7 0.9 - - - +
161D ALA* 3.8 15.8 - - + +
162D ALA 3.7 9.4 - - - +
163D PHE* 3.9 20.0 - - + -
185D PRO* 3.7 28.1 - - + +
186D VAL* 3.7 31.4 - - - +
187D GLY* 3.7 6.1 - - - +
242D PHE* 4.3 7.4 - - + -
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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