Contacts of the helix formed by residues 74 - 84 (chain I) in PDB entry 2J28
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 PRO 74 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B U 3.4 17.9 - - - +
11I GLN* 3.4 31.4 - - + +
53I PRO* 3.5 11.7 - - + +
55I PRO* 3.4 17.9 - - + -
72I THR 3.7 0.2 - - - -
73I PRO* 1.3 89.5 - - + +
75I ALA* 1.3 64.8 + - - +
76I ALA* 4.4 5.2 - - + +
77I VAL* 3.3 25.5 + - + +
78I LEU* 3.0 20.8 + - - +
112I LYS* 3.9 0.4 - - - +
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Residues in contact with ALA 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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1059B G 3.7 16.6 - - - +
1060B U 2.7 28.7 + - - +
73I PRO 3.7 1.2 + - - -
74I PRO* 1.3 68.9 - - - +
76I ALA* 1.3 59.1 + - - +
78I LEU* 3.3 7.8 + - - +
79I LEU* 2.8 36.8 + - - +
108I ILE* 4.9 1.3 - - - -
112I LYS* 4.1 5.5 - - + +
116I MET* 4.6 3.6 - - + -
128I ILE* 4.6 13.2 - - + -
131I THR* 3.8 15.9 - - + +
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060B U 4.0 3.1 + - - +
1062B G 4.4 3.1 - - - +
1063B G 3.0 32.1 - - - +
74I PRO* 3.3 4.4 - - + +
75I ALA* 1.3 78.9 - - - +
77I VAL* 1.3 66.7 + - + +
79I LEU* 4.6 0.2 - - - -
80I LYS* 3.0 16.6 + - - +
131I THR* 4.6 3.7 + - - -
135I MET* 3.0 43.8 - - + +
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Residues in contact with VAL 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I LEU* 5.6 0.2 - - + -
53I PRO* 3.2 42.2 - - + -
73I PRO* 5.0 4.7 - - + -
74I PRO* 3.6 28.9 - - + +
75I ALA 3.2 0.6 - - - -
76I ALA* 1.3 74.6 - - + +
78I LEU* 1.3 67.9 + - - +
80I LYS* 2.9 26.4 + - + +
81I LYS* 3.0 24.0 + - + +
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Residues in contact with LEU 78 (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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52I LEU* 5.0 0.2 - - + -
73I PRO* 3.3 44.0 - - + +
74I PRO 3.0 17.2 + - - +
75I ALA 3.7 1.3 - - - +
77I VAL* 1.3 76.9 - - + +
79I LEU* 1.3 58.6 + - - +
81I LYS* 3.4 33.0 + - - +
82I ALA* 3.0 29.8 + - - +
108I ILE* 3.5 37.7 - - + +
111I THR* 4.2 17.0 - - + -
112I LYS* 3.6 14.8 - - + -
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Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ALA 2.8 20.8 + - - +
78I LEU* 1.3 76.7 - - - +
80I LYS* 1.3 57.7 + - - +
83I ALA* 2.8 32.9 + - - +
100I ILE* 3.2 14.0 - - + +
105I LEU* 3.5 24.0 - - + -
108I ILE* 3.3 22.9 - - + -
128I ILE* 3.7 6.5 - - + +
131I THR* 2.7 30.3 - - - +
132I ALA* 3.3 20.4 - - + +
135I MET* 3.2 28.7 - - - -
137I LEU* 3.5 7.2 - - + -
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Residues in contact with LYS 80 (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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1063B G 4.3 6.3 + - - -
1064B C 3.6 21.9 + - - -
76I ALA* 3.0 29.2 + - - +
77I VAL* 2.9 19.2 + - + +
79I LEU* 1.3 74.3 - - - +
81I LYS* 1.3 53.8 + - + +
83I ALA 3.2 0.9 + - - -
84I GLY 2.7 29.6 + - - -
85I ILE* 2.9 35.5 + - + +
86I LYS 3.4 25.4 - - - +
87I SER* 3.7 15.3 - - - +
88I GLY 3.8 3.6 - - - +
135I MET* 3.4 16.6 - - + +
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Residues in contact with LYS 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I LEU* 3.2 51.3 - - + +
77I VAL* 3.0 21.2 + - + +
78I LEU* 3.4 37.2 - - - +
80I LYS* 1.3 75.2 - - + +
82I ALA* 1.3 58.2 + - - +
84I GLY* 2.8 25.0 + - - -
85I ILE 5.0 0.7 - - - -
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Residues in contact with ALA 82 (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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78I LEU 3.0 18.6 + - - +
81I LYS* 1.3 77.5 - - - +
83I ALA* 1.3 61.9 + - - +
84I GLY* 4.4 0.3 - - - -
99I LYS 4.7 0.9 - - - +
100I ILE* 3.5 18.6 - - + -
104I GLN* 3.1 37.3 + - + +
108I ILE* 4.1 12.6 - - + -
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Residues in contact with ALA 83 (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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79I LEU 2.8 22.6 + - - +
80I LYS 3.6 3.6 - - - +
82I ALA* 1.3 74.2 - - - +
84I GLY* 1.3 61.0 + - - +
85I ILE* 3.5 31.3 + - + +
98I GLY* 5.6 0.3 - - - -
99I LYS* 3.8 28.4 + - - +
100I ILE* 3.8 9.8 - - + +
137I LEU* 4.1 9.0 - - + -
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Residues in contact with GLY 84 (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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80I LYS 2.7 5.5 + - - -
81I LYS* 2.8 15.5 + - - -
82I ALA 4.4 0.4 - - - -
83I ALA* 1.3 79.8 - - - +
85I ILE* 1.3 61.0 + - - +
86I LYS* 4.3 1.4 + - - +
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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