Contacts of the helix formed by residues 76 - 87 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C LEU* 3.6 23.1 - - + -
70C ARG* 3.8 20.6 + - - -
73C GLN* 3.0 33.3 + - - -
74C ILE* 3.6 24.7 - - + -
75C ILE* 1.3 74.4 - - - +
77C PRO* 1.4 61.9 - - + +
78C LYS* 3.1 11.2 - - + +
79C ASP* 2.8 29.4 + - - +
80C SER* 2.9 11.9 + - - -
237C THR* 3.6 35.0 - - + -
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Residues in contact with PRO 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 3.6 41.5 - - + +
64C ILE* 4.0 28.7 - - + -
65C LEU* 3.8 23.1 - - + -
76C TYR* 1.4 85.4 - - + +
78C LYS* 1.3 62.3 + - - +
80C SER* 3.1 11.6 - - - +
81C PHE* 2.9 46.2 + - + +
82D TYR* 4.5 1.1 - - - -
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 5.2 0.4 + - - -
76C TYR* 3.1 7.1 - - + +
77C PRO* 1.3 78.8 - - - +
79C ASP* 1.3 75.3 + - - +
81C PHE* 5.0 0.7 - - - +
82C TYR* 4.2 6.8 + - - +
215C ILE* 2.6 49.1 + - + +
216C LEU* 5.0 0.4 - - - +
217C HIS* 3.5 58.7 + - + +
234C VAL* 4.6 14.6 - - + +
236C HIS* 5.8 0.6 - - - +
237C THR* 2.9 44.3 + - - +
238C ALA 5.5 0.8 + - - -
82D TYR* 4.8 4.0 - - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 4.0 12.7 - - + +
76C TYR 2.8 18.1 + - - +
78C LYS* 1.3 95.0 + - - +
80C SER* 1.3 58.4 + - - +
81C PHE 3.3 0.4 - - - -
82C TYR* 3.1 6.1 + - - +
83C ILE* 2.9 39.8 + - + +
189C LEU* 4.4 8.7 - - - +
215C ILE* 3.9 15.6 + - - +
237C THR* 2.6 30.3 + - - +
238C ALA 4.4 4.4 + - - +
240C LEU* 3.9 18.0 - - + +
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 5.0 0.5 - - - +
75C ILE* 3.9 10.4 + - - -
76C TYR 2.9 12.7 + - - -
77C PRO* 3.1 23.4 - - - +
79C ASP* 1.3 70.3 - - - +
81C PHE* 1.3 66.5 + - - +
83C ILE* 3.7 10.3 - - - +
84C ALA* 3.0 27.7 + - - +
104C ALA 4.7 0.9 + - - -
105C LEU* 3.7 25.8 - - - +
108C VAL* 3.4 23.8 - - - +
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Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 4.1 14.1 - - + -
61C GLU* 3.9 33.7 - - + -
64C ILE* 4.6 0.7 - - + -
77C PRO* 2.9 29.5 + - + +
78C LYS 5.0 0.2 - - - +
80C SER* 1.3 80.7 - - - +
82C TYR* 1.3 61.4 + - - +
85C LEU* 3.9 9.0 + - - +
108C VAL* 3.7 27.1 - - + -
81D PHE* 3.8 21.0 - - - +
82D TYR* 3.7 34.3 - + + -
85D LEU* 3.5 55.1 - - + +
86D LYS* 3.6 7.9 - - + -
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LYS 4.2 5.0 + - - +
79C ASP 3.1 8.9 + - - +
81C PHE* 1.3 78.5 - - - +
83C ILE* 1.3 60.0 + - - +
85C LEU 3.4 1.6 + - - -
86C LYS* 2.9 61.6 + - + +
211C GLU* 5.0 2.1 + - - -
213C VAL* 4.4 10.6 - - + +
215C ILE* 3.7 25.8 - - + -
240C LEU* 4.6 1.6 - - + -
242C PHE* 4.0 19.3 - + - -
61D GLU* 2.5 31.1 + - - -
77D PRO 4.5 7.2 - - - -
78D LYS* 4.7 4.3 - - - +
81D PHE* 3.6 33.2 - + + -
82D TYR* 5.2 1.5 - - + +
217D HIS* 3.5 31.4 + + + +
219D HIS* 5.2 5.0 - - - -
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Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 4.2 10.5 - - + -
79C ASP* 2.9 37.7 + - + +
80C SER* 3.7 9.2 - - - +
82C TYR* 1.3 75.4 - - - +
84C ALA* 1.3 59.5 + - - +
86C LYS* 3.3 0.7 + - - +
87C LEU* 2.9 43.5 + - + +
105C LEU* 4.0 15.3 - - + -
109C LEU* 4.8 0.9 - - + -
163C PHE* 3.6 46.7 - - + -
240C LEU* 4.1 11.9 - - + -
242C PHE* 3.9 24.7 - - + -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER 3.0 17.2 + - - +
81C PHE 4.3 3.4 - - - +
83C ILE* 1.3 81.3 - - - +
85C LEU* 1.3 61.5 + - - +
87C LEU 3.7 1.0 + - - -
89C LEU* 3.4 39.2 + - + +
108C VAL* 3.7 20.9 - - + +
109C LEU* 4.4 12.1 - - + -
112C VAL* 4.0 21.5 - - + -
85D LEU* 4.6 1.1 - - + -
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Residues in contact with LEU 85 (chain C).
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 3.9 2.6 + - - +
82C TYR 3.4 1.8 + - - -
83C ILE 3.3 0.2 - - - -
84C ALA* 1.3 75.4 - - - +
86C LYS* 1.3 60.1 + - - +
87C LEU 3.2 1.6 - - - -
88C ASN* 3.0 19.5 + - - +
89C LEU 4.3 9.0 - - - +
112C VAL* 4.1 17.7 - - + -
59D THR* 5.7 0.5 - - - -
60D LEU* 4.5 22.0 - - + +
61D GLU 5.3 0.7 + - - -
81D PHE* 3.6 63.6 - - + +
84D ALA* 4.7 0.9 - - + -
85D LEU* 3.9 18.8 - - + -
108D VAL* 3.9 14.6 - - + -
111D GLU* 5.1 4.5 - - + -
112D VAL* 3.9 24.0 - - + -
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 2.9 47.7 + - + +
83C ILE 3.6 3.6 - - - +
85C LEU* 1.3 71.9 - - - +
87C LEU* 1.3 57.2 + - - +
88C ASN* 3.0 12.8 + - - +
185C PRO* 4.7 3.3 - - - +
211C GLU* 2.7 39.0 + - - -
242C PHE* 3.6 42.4 - - + -
18D LYS* 4.0 3.8 - - - +
59D THR* 4.4 16.7 + - - +
61D GLU* 2.7 34.4 + - + +
62D GLU* 5.2 1.4 + - - -
81D PHE* 3.5 7.2 - - + -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 2.9 39.3 + - + +
84C ALA 3.9 5.2 - - - +
85C LEU 3.2 0.2 - - - -
86C LYS* 1.3 72.7 - - - +
88C ASN* 1.3 69.1 + - - +
89C LEU* 3.3 17.2 + - + +
93C LYS* 5.9 0.2 - - - +
95C VAL* 4.7 1.8 - - + -
109C LEU* 4.6 4.9 - - + -
160C HIS 4.6 1.2 - - - +
161C ALA* 3.7 24.1 - - + +
162C ALA 3.8 9.4 - - - +
163C PHE* 4.0 19.7 - - + -
185C PRO* 3.8 20.1 - - + +
186C VAL* 3.7 34.5 - - - +
187C GLY 3.7 3.6 - - - +
242C PHE* 4.2 12.1 - - + -
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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