Contacts of the strand formed by residues 65 - 74 (chain G) in PDB entry 5JLH
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 PHE 65 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G TRP* 3.8 9.8 - - + -
58G VAL 3.4 17.7 - - - +
59G PRO* 4.0 24.2 - - + -
63G HIS* 4.3 1.1 - - - -
64G GLY* 1.3 85.1 - - - +
66G GLU* 1.3 60.4 + - - +
95G GLN 4.5 2.2 - - - -
97G GLN* 4.2 9.9 - - + -
118G GLU* 3.6 36.6 - - + -
119G ALA* 3.5 42.6 - - + +
122G LEU* 4.5 14.0 - - + +
123G HIS* 6.0 0.2 - - - +
126G ARG* 3.3 27.0 + - - -
713G LEU* 3.6 25.8 - - + -
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Residues in contact with GLU 66 (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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57G TRP* 3.1 8.9 - - - -
58G VAL* 2.8 44.7 + - + +
60G SER* 3.2 31.2 + - - +
62G LEU* 4.4 8.1 - - - +
63G HIS* 4.2 25.2 - - + +
65G PHE* 1.3 73.9 - - - +
67G ALA* 1.3 64.7 + - - +
82G LEU* 3.8 27.9 - - - +
84G GLU* 5.4 7.3 - - - +
87G ARG* 5.4 3.1 + - - -
126G ARG* 5.0 2.5 - - - +
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Residues in contact with ALA 67 (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* 5.5 6.7 - - + -
56G VAL 4.5 1.1 - - - -
57G TRP* 3.2 28.1 - - + +
66G GLU* 1.3 77.4 - - - +
68G ALA* 1.3 62.7 + - - +
82G LEU* 4.0 2.4 - - - +
83G ALA* 3.1 35.9 + - + +
84G GLU 4.9 0.2 + - - -
99G MET* 4.6 14.4 - - + -
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Residues in contact with ALA 68 (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* 4.1 6.6 - - - +
56G VAL* 2.5 50.7 + - - +
58G VAL* 3.9 8.3 - - + -
67G ALA* 1.3 76.1 - - - +
69G ALA* 1.3 58.4 + - - +
70G LEU 3.7 0.5 + - - -
80G VAL* 3.2 22.3 - - + +
81G GLU 3.2 9.0 - - - +
82G LEU* 3.5 21.8 - - + -
83G ALA 4.1 1.6 - - - +
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Residues in contact with ALA 69 (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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53G ARG* 3.9 27.4 - - + +
54G ARG 3.5 6.1 - - - -
55G LEU* 3.6 20.5 - - + +
68G ALA* 1.3 69.9 - - - +
70G LEU* 1.3 63.0 + - - +
71G ARG* 3.5 4.7 + - + +
80G VAL* 3.0 3.5 - - - +
81G GLU* 2.5 57.3 + - + +
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Residues in contact with LEU 70 (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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54G ARG* 2.8 42.4 + - + +
56G VAL* 4.2 20.9 - - + -
68G ALA 3.7 2.0 + - - -
69G ALA* 1.3 70.3 - - - +
71G ARG* 1.3 71.4 + - - +
72G ASP 2.7 13.5 + - - +
73G GLU* 3.7 36.1 - - + +
78G ALA* 4.5 12.6 - - + -
79G GLU 2.6 28.9 - - - +
80G VAL* 3.8 10.5 - - + +
93G ARG* 4.6 19.1 - - + -
96G ILE* 5.9 4.3 - - + -
98G ARG* 6.0 3.4 - - - +
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Residues in contact with ARG 71 (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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53G ARG* 3.4 48.8 + - + +
54G ARG* 6.2 0.4 - - - +
69G ALA* 4.5 5.2 - - + +
70G LEU* 1.3 87.0 - - - +
72G ASP* 1.3 64.8 + - - +
73G GLU* 3.5 6.2 + - - +
79G GLU 4.8 0.7 - - - +
81G GLU* 3.6 39.1 + - + -
88G ARG* 4.7 13.3 - - - +
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Residues in contact with ASP 72 (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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70G LEU 2.7 16.9 + - - +
71G ARG* 1.3 76.3 - - - +
73G GLU* 1.3 68.3 + - - +
77G GLU 5.4 0.7 - - - +
78G ALA* 3.4 4.7 - - - +
79G GLU* 3.0 48.7 + - + +
88G ARG* 3.6 22.0 - - - +
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Residues in contact with GLU 73 (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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54G ARG* 3.0 31.8 + - - -
70G LEU* 3.7 18.9 - - + +
71G ARG 3.5 4.0 + - - +
72G ASP* 1.3 85.7 + - - +
74G GLY* 1.3 60.5 + - - +
75G GLU 5.7 0.2 - - - +
77G GLU 3.8 6.7 - - - -
78G ALA* 4.1 6.7 - - + +
93G ARG* 4.3 17.8 + - - -
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Residues in contact with GLY 74 (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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73G GLU* 1.3 80.3 - - - +
75G GLU* 1.3 71.6 + - - +
77G GLU* 2.5 31.4 + - - +
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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
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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