Contacts of the strand formed by residues 65 - 69 (chain H) in PDB entry 2Q9Q
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 LYS 65 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34H VAL 3.5 3.8 - - - +
35H ARG* 3.6 40.5 - - + +
63H GLY 3.6 6.7 + - - +
64H SER* 1.3 71.6 - - - +
66H LEU* 1.3 72.4 + - - +
87H GLU* 2.9 31.5 + - - +
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Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H PRO* 3.4 3.5 - - - +
34H VAL* 2.7 51.3 + - + +
36H THR* 4.3 14.1 - - + -
40H MET* 6.3 0.9 - - - -
46H PHE* 3.9 31.0 - - + -
60H VAL* 4.2 25.6 - - + -
64H SER* 4.3 9.6 - - - +
65H LYS* 1.3 86.9 - - - +
67H GLU* 1.3 64.3 + - - +
68H LEU* 4.3 18.6 - - + -
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Residues in contact with GLU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LYS* 3.4 40.5 + - + +
32H LEU* 3.2 10.2 - - - +
33H PRO* 4.7 14.9 - - + +
66H LEU* 1.3 78.1 - - - +
68H LEU* 1.3 65.4 + - - +
69H PRO* 4.5 0.3 - - - +
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Residues in contact with LEU 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 5.1 8.1 - - + -
64G PHE* 5.3 4.3 - - + -
31H LYS* 3.9 3.8 - - - -
32H LEU* 2.8 40.8 + - - +
34H VAL* 3.6 27.1 - - + -
36H THR* 6.2 2.0 - - + -
40H MET* 6.3 1.8 - - - -
66H LEU* 4.0 20.1 - - + -
67H GLU* 1.3 81.7 - - - +
69H PRO* 1.3 72.6 - - + +
72H LEU* 4.1 27.4 - - + -
73H ALA* 4.7 7.6 - - + -
76H LEU* 4.6 5.2 - - + -
84H LEU* 4.1 19.7 - - + -
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Residues in contact with PRO 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 5.1 11.2 - - + -
29H HIS* 3.5 24.5 - - + +
30H GLU 3.5 8.1 - - - +
31H LYS* 4.2 14.8 - - + -
67H GLU 4.5 1.8 - - - +
68H LEU* 1.3 91.8 - - + +
70H LEU* 1.3 66.0 + - - +
71H TRP* 3.3 37.7 - - + +
72H LEU* 3.0 26.2 + - + +
73H ALA* 3.0 10.9 + - - +
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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