Contacts of the helix formed by residues 68 - 75 (chain I) in PDB entry 2YW7
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 68 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21I LEU* 3.9 40.2 - - + +
24I GLN* 4.1 4.0 - - + -
25I LEU* 3.6 16.2 - - + -
28I TYR* 3.6 28.9 - - + -
64I TYR 2.5 28.3 + - - +
65I ALA* 3.5 17.0 - - - +
67I GLU* 1.3 71.6 - - - +
69I ALA* 1.3 58.4 + - - +
71I ARG* 4.2 4.6 - - - +
72I ILE* 3.2 25.3 + - - +
137I LEU* 4.6 6.7 - - + +
138I LEU* 4.6 5.2 - - + -
141I HIS* 4.8 3.4 - - + -
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Residues in contact with ALA 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TRP* 3.8 35.6 - - + +
25I LEU* 4.2 5.8 - - + -
65I ALA 3.1 21.6 + - - +
66I ASP 3.3 4.2 + - - +
67I GLU 3.1 0.8 - - - -
68I VAL* 1.3 78.4 - - - +
70I GLU* 1.3 57.1 + - - +
71I ARG 2.9 9.4 + - - -
72I ILE* 4.1 7.2 - - - +
73I ALA* 3.1 26.0 + - - +
79I PRO* 4.1 8.7 - - + +
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Residues in contact with GLU 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TRP* 5.6 3.8 - - + -
66I ASP* 2.8 34.3 + - + +
67I GLU* 3.5 16.3 + - + +
69I ALA* 1.3 75.1 - - - +
71I ARG* 1.3 57.0 + - - +
73I ALA* 4.4 5.8 - - - +
74I THR* 3.7 18.2 + - - +
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Residues in contact with ARG 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I LEU* 4.0 18.8 - - + -
67I GLU 3.6 12.0 + - - +
68I VAL* 4.4 6.7 - - - +
69I ALA 2.9 1.8 - - - -
70I GLU* 1.3 78.7 - - - +
72I ILE* 1.3 65.2 + - - +
73I ALA 3.0 1.3 - - - -
74I THR* 2.9 36.1 + - - +
75I LEU* 3.2 30.3 + - + +
131I ASP* 3.1 30.9 + - - -
132I LEU* 4.5 9.9 - - - +
133I VAL* 4.0 29.1 - - - +
134I SER* 4.7 7.2 - - - +
137I LEU* 5.1 11.2 - - + -
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ALA* 4.4 7.9 - - + +
21I LEU* 3.7 20.9 - - + +
22I GLN* 3.4 37.7 - - + +
25I LEU* 3.8 20.4 - - + -
68I VAL 3.2 19.9 + - - +
69I ALA* 3.4 5.3 + - - +
71I ARG* 1.3 76.9 - - - +
73I ALA* 1.3 60.8 + - - +
75I LEU* 3.9 10.6 + - - +
77I LYS* 3.1 47.7 + - + +
78I SER 4.1 3.1 - - - +
79I PRO* 4.0 17.5 - - + -
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Residues in contact with ALA 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TRP* 4.7 9.0 - - + +
99D ARG* 2.3 38.2 + - - +
69I ALA 3.1 17.2 + - - +
70I GLU* 4.5 5.8 - - - +
71I ARG 3.0 0.2 - - - -
72I ILE* 1.3 77.1 - - - +
74I THR* 1.3 60.8 + - - +
76I GLY 3.0 4.7 + - - -
77I LYS 3.5 10.5 - - - +
79I PRO* 4.3 10.4 - - + +
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Residues in contact with THR 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG* 4.3 2.8 + - - +
70I GLU 3.7 11.1 + - - +
71I ARG* 2.9 42.5 + - - +
73I ALA* 1.3 79.7 - - - +
75I LEU* 1.3 72.5 + - + +
76I GLY* 2.9 6.6 + - - -
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ALA* 4.9 2.0 - - + +
17I VAL* 5.3 2.2 - - + -
18I ALA* 3.3 37.0 - - + +
21I LEU* 4.9 2.2 - - + -
71I ARG* 3.2 55.8 + - + +
72I ILE 4.0 2.5 - - - +
73I ALA 3.4 0.2 - - - -
74I THR* 1.3 79.0 - - + +
76I GLY* 1.3 65.0 + - - +
77I LYS* 3.7 22.2 + - - +
131I ASP* 4.3 15.3 - - - +
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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