Contacts of the helix formed by residues 63 - 71 (chain D) in PDB entry 2WY2
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 MET 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D GLU* 3.4 35.4 - - + +
56D LEU* 4.4 2.5 - - - -
60D ILE* 3.0 37.3 + - - +
61D ALA 2.9 0.2 + - - -
62D TYR* 1.3 109.2 - - + +
64D LEU* 1.3 63.3 + - - +
65D PRO* 3.4 2.0 - - - -
66D GLU* 3.1 37.8 + - + +
67D ILE* 3.1 30.5 + - + +
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Residues in contact with LEU 64 (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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56D LEU* 3.9 16.2 - - + +
61D ALA 2.9 15.2 + - - +
63D MET* 1.3 74.9 - - - +
65D PRO* 1.4 70.1 - - + +
67D ILE* 3.2 2.6 + - - +
68D GLN* 2.9 57.4 + - - +
76D VAL* 3.8 31.9 - - + +
77D GLU* 4.4 5.8 - - - -
78D VAL* 4.2 16.2 - - + +
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Residues in contact with PRO 65 (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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61D ALA 4.5 0.4 - - - +
62D TYR* 3.8 12.1 - - - +
63D MET 3.6 3.1 - - - -
64D LEU* 1.4 94.9 - - + +
66D GLU* 1.3 60.9 + - + +
68D GLN* 3.4 14.1 + - - +
69D ARG* 3.2 45.3 + - - +
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Residues in contact with GLU 66 (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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62D TYR* 4.9 5.6 - - - +
63D MET* 3.1 36.4 + - + +
65D PRO* 1.3 78.4 - - + +
67D ILE* 1.3 67.1 + - + +
69D ARG* 3.4 23.3 + - - +
70D LEU* 3.1 23.9 + - + +
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Residues in contact with ILE 67 (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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41D GLU* 5.7 2.0 - - + +
44D ALA* 4.2 23.3 - - + -
54D VAL* 4.4 7.6 - - + -
56D LEU* 3.5 33.4 - - + -
60D ILE* 5.0 5.2 - - + -
63D MET* 3.1 33.1 + - + +
64D LEU 3.9 2.9 - - - +
66D GLU* 1.3 75.6 - - + +
68D GLN* 1.3 60.0 + - - +
70D LEU* 3.1 12.4 + - + +
71D LEU* 2.9 49.2 + - + +
76D VAL* 3.9 22.7 - - + -
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Residues in contact with GLN 68 (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 LEU* 2.9 51.7 + - + +
65D PRO* 3.7 15.8 - - - +
66D GLU 3.3 0.2 - - - -
67D ILE* 1.3 76.1 - - - +
69D ARG* 1.3 60.4 + - + +
71D LEU 3.3 19.7 - - - +
72D PRO* 3.3 7.8 - - - +
76D VAL* 4.0 27.3 + - + -
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Residues in contact with ARG 69 (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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65D PRO* 3.2 33.4 + - - +
66D GLU* 3.7 30.8 - - - +
67D ILE 3.3 0.2 - - - -
68D GLN* 1.3 76.4 - - + +
70D LEU* 1.3 61.5 + - - +
72D PRO* 3.6 13.9 - - - +
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Residues in contact with LEU 70 (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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44D ALA* 4.5 2.9 - - + -
45D GLY* 3.6 36.6 - - - +
49D GLN* 5.9 0.7 + - - -
66D GLU* 3.1 15.4 + - + +
67D ILE* 3.4 20.9 - - + +
69D ARG* 1.3 79.0 - - - +
71D LEU* 1.3 66.8 + - + +
72D PRO* 3.4 7.1 - - - +
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Residues in contact with LEU 71 (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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44D ALA 3.6 19.3 - - - +
45D GLY* 4.2 11.2 - - - +
48D GLY* 4.0 12.1 - - - -
49D GLN* 3.9 35.9 - - + +
54D VAL* 4.0 17.3 - - + -
67D ILE* 2.9 29.2 + - + +
68D GLN* 3.3 8.4 - - - +
70D LEU* 1.3 87.9 - - + +
72D PRO* 1.4 62.2 - - - +
73D ASN* 3.1 11.0 + - - +
74D LYS* 3.3 29.5 + - + +
76D VAL* 4.3 6.0 - - + +
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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