Contacts of the strand formed by residues 78 - 84 (chain G) in PDB entry 2HAK
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 GLU 78 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56G GLN* 2.8 38.4 + - - +
69G LEU* 3.2 21.0 - - + +
70G ALA 2.9 6.6 - - - +
71G ARG* 2.6 45.5 + - - +
76G GLY 3.6 0.6 + - - -
77G ARG* 1.3 70.7 - - - +
79G VAL* 1.3 68.0 + - - +
116G PHE* 5.0 1.6 - - - -
131G TYR* 3.7 24.1 + - + +
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Residues in contact with VAL 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G TYR* 3.6 29.4 - - + -
69G LEU* 3.5 6.1 - - - +
70G ALA* 2.7 46.0 + - + +
77G ARG* 4.2 8.5 - - + +
78G GLU* 1.3 81.2 - - - +
80G ALA* 1.3 57.4 + - - +
81G VAL* 4.2 2.2 - - + -
116G PHE* 3.7 25.8 - - + -
128G VAL* 3.6 14.8 - - + -
129G MET 3.4 10.3 - - - +
131G TYR* 3.9 8.5 - - - +
360G LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ILE* 4.6 9.4 - - + -
67G VAL* 4.0 17.7 - - + -
68G LYS 3.5 6.3 - - - +
69G LEU* 4.7 1.3 - - - +
79G VAL* 1.3 72.8 - - - +
81G VAL* 1.3 59.9 + - - +
82G LYS 4.1 0.4 - - - -
128G VAL* 3.5 2.1 - - - +
129G MET* 2.8 52.5 + - + +
130G GLU 4.0 9.2 - - - +
131G TYR* 3.9 9.3 - - + +
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Residues in contact with VAL 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE* 4.6 8.5 - - + -
53G TYR* 4.8 5.2 - - + -
55G LEU* 4.2 10.5 - - + -
66G LYS 3.6 0.9 - - - +
67G VAL* 3.4 3.8 - - - +
68G LYS* 2.8 39.2 + - + +
70G ALA* 3.5 31.9 - - + -
79G VAL* 4.2 7.9 - - + -
80G ALA* 1.3 74.4 - - - +
82G LYS* 1.3 60.5 + - - +
83G ILE* 3.6 8.3 + - + +
126G TYR* 4.0 34.5 - - + -
127G LEU 3.1 9.2 - - - +
128G VAL* 4.4 13.0 - - + -
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Residues in contact with LYS 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ALA* 4.3 5.8 - - + -
66G LYS 3.2 6.1 - - - +
67G VAL* 3.5 27.7 - - + +
80G ALA 4.1 1.0 - - - -
81G VAL* 1.3 70.7 - - - +
83G ILE* 1.3 61.6 - - - +
84G ILE* 3.6 24.6 + - + +
100G GLU* 5.2 1.0 + - - -
104G MET* 4.1 22.0 - - - +
125G LEU 3.6 1.6 - - - +
126G TYR* 3.4 3.6 - - - -
127G LEU* 2.7 47.2 + - + +
129G MET* 5.1 14.3 - - - +
193G ASP* 4.1 17.4 + - - -
200G PHE* 3.1 35.1 + - + +
201G THR* 4.9 4.0 - - - +
202G VAL* 5.5 1.1 - - - -
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Residues in contact with ILE 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU* 5.6 5.6 - - + -
64G PHE 4.0 0.9 - - - +
65G ALA* 3.6 5.7 - - - -
66G LYS* 2.7 48.3 + - + +
68G LYS* 4.0 29.4 - - + -
81G VAL* 4.1 15.7 - - + +
82G LYS* 1.3 71.0 - - - +
84G ILE* 1.3 65.1 + - - +
85G ASP* 3.9 5.2 + - + +
124G THR* 3.6 19.5 - - + +
125G LEU 3.6 3.1 - - - -
126G TYR* 3.7 29.6 - - + +
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Residues in contact with ILE 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G PHE 4.3 4.0 - - - +
65G ALA* 4.4 6.5 - - + -
82G LYS* 3.6 38.1 - - + +
83G ILE* 1.3 78.3 - - - +
85G ASP* 1.3 61.2 + - - +
86G LYS* 3.1 18.9 + - + +
89G LEU* 4.8 7.9 - - + -
97G LEU* 4.0 40.8 - - + -
124G THR* 3.1 6.1 + - - -
125G LEU* 2.7 45.6 + - + +
127G LEU* 4.4 10.1 - - + -
200G PHE* 4.3 22.4 - - + -
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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
------------------------------------------------------------
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