Contacts of the helix formed by residues 92 - 107 (chain J) in PDB entry 7C97
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 TYR 92 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575F GLU* 5.5 6.7 - - - +
578F LYS* 6.6 0.2 - - - -
82I ARG* 5.6 0.9 - - - +
90J PRO* 4.2 1.9 - - - +
91J VAL* 1.3 107.0 - - + +
93J PRO* 1.3 70.2 - - + +
94J VAL* 2.9 25.4 + - + -
95J ALA* 3.3 13.5 + - + +
96J ARG* 3.7 11.0 + - - +
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Residues in contact with PRO 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F GLU* 5.5 8.7 - - - +
578F LYS* 6.5 0.7 - - - -
78I TYR* 3.4 20.2 - - + +
81I GLU* 3.3 30.1 - - + +
82I ARG* 3.5 46.4 - - + +
91J VAL 4.5 2.0 - - - +
92J TYR* 1.3 88.4 - - + +
94J VAL* 1.3 62.9 + - - +
95J ALA 3.4 0.4 + - - -
96J ARG* 4.1 11.9 - - + +
97J GLY 3.7 8.0 + - - -
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Residues in contact with VAL 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I GLU* 5.0 14.2 - - + +
78I TYR* 4.4 14.5 - - - +
82I ARG* 3.1 29.8 - - - +
92J TYR* 4.0 22.9 - - + +
93J PRO* 1.3 76.7 - - - +
95J ALA* 1.3 71.3 + - + +
97J GLY* 3.8 5.7 + - - -
98J GLU* 3.6 16.8 + - - +
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Residues in contact with ALA 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J PRO* 3.4 24.5 - - + +
92J TYR* 3.3 4.7 + - + +
94J VAL* 1.3 81.8 - - + +
96J ARG* 1.3 62.1 + - - +
97J GLY 3.2 1.8 - - - -
98J GLU* 2.8 43.5 + - - +
99J SER* 2.9 12.5 + - - +
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Residues in contact with ARG 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I GLU* 2.9 33.8 + - + +
81J GLU* 3.9 21.0 + - - -
89J MET* 3.9 24.5 - - + +
90J PRO* 3.3 46.4 + - + +
91J VAL 4.5 5.3 + - - -
92J TYR 3.7 17.2 + - - +
93J PRO* 4.3 9.2 - - + +
94J VAL 3.5 0.8 - - - -
95J ALA* 1.3 77.0 - - - +
97J GLY* 1.3 53.3 + - - +
99J SER* 4.1 0.6 - - - +
100J ARG* 2.7 76.9 + - + +
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Residues in contact with GLY 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I GLU* 6.0 2.0 - - - -
69I LEU* 5.0 9.4 - - - +
74I ILE* 4.8 5.6 - - - +
78I TYR* 4.6 17.4 - - - -
93J PRO 3.7 8.5 + - - -
94J VAL 3.8 4.0 + - - -
95J ALA 3.2 0.8 - - - -
96J ARG* 1.3 78.2 - - - +
98J GLU* 1.3 56.8 + - - +
100J ARG* 3.8 6.4 - - - +
101J LEU* 3.0 35.0 + - - +
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Residues in contact with GLU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I GLU* 4.6 21.3 - - - +
67I LEU* 6.5 0.7 - - + -
94J VAL* 3.6 11.7 + - - +
95J ALA* 2.8 37.8 + - - +
97J GLY* 1.3 76.5 - - - +
99J SER* 1.3 56.8 + - - +
101J LEU* 3.2 2.6 + - - -
102J TYR* 2.7 57.6 + - + +
150J LEU* 5.5 7.8 - - + +
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Residues in contact with SER 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J MET* 4.0 23.1 - - - -
90J PRO* 3.8 12.2 - - - +
95J ALA* 2.9 13.2 + - - +
96J ARG 4.1 0.7 - - - -
98J GLU* 1.3 76.3 + - - +
100J ARG* 1.3 63.6 + - - +
102J TYR* 3.9 7.5 - - - +
103J MET* 3.0 31.2 + - - +
155J SER* 5.5 1.3 + - - -
156J LEU* 6.1 0.2 - - - -
157J VAL* 4.9 22.5 - - - +
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Residues in contact with ARG 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I ILE* 3.0 34.7 - - + +
77I GLU* 3.1 38.6 + - - +
81I GLU* 4.5 3.6 + - - +
100I ARG* 3.1 22.6 - - - +
73J ARG* 4.3 4.2 + - - +
77J GLU* 2.7 37.6 + - - +
81J GLU* 5.0 2.4 + - - -
89J MET* 4.2 16.8 - - + +
96J ARG* 2.7 66.8 + - + +
97J GLY* 4.1 5.4 - - - +
99J SER* 1.3 72.9 - - - +
101J LEU* 1.3 56.7 + - - +
103J MET* 3.4 20.5 - - - +
104J HIS* 3.8 5.2 + - - +
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Residues in contact with LEU 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I LEU* 4.9 10.8 - - + -
68I THR 3.6 23.8 - - - +
69I LEU* 4.1 22.7 - - + -
70I TRP* 3.9 37.9 - - + +
74I ILE* 4.5 13.2 - - + -
97J GLY 3.0 20.3 + - - +
98J GLU* 3.8 3.1 - - - +
100J ARG* 1.3 77.7 - - - +
102J TYR* 1.3 70.8 + - + +
103J MET 3.2 1.8 - - - -
104J HIS* 2.9 19.0 + - + +
105J ARG* 3.1 18.9 + - + +
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Residues in contact with TYR 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I LEU* 5.0 18.2 - - + +
98J GLU* 2.7 41.6 + - + +
99J SER* 3.9 6.1 - - - +
101J LEU* 1.3 78.9 - - + +
103J MET* 1.3 61.5 + - - +
105J ARG* 3.1 48.6 + - - +
106J ILE* 3.4 9.1 - - - +
149J PHE* 4.1 24.8 - + + -
150J LEU* 3.4 32.3 - - + +
157J VAL* 4.5 14.6 - - + -
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Residues in contact with MET 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J ARG* 3.6 32.3 - - - +
77J GLU* 5.0 8.7 - - + +
89J MET* 4.6 14.4 - - - -
99J SER 3.0 21.8 + - - +
100J ARG* 3.4 20.2 - - - +
102J TYR* 1.3 74.4 - - - +
104J HIS* 1.3 63.7 + - - +
105J ARG 3.3 0.2 - - - -
106J ILE* 3.5 9.1 - - - +
107J GLU* 3.1 31.5 + - + +
156J LEU* 4.9 13.5 - - + +
157J VAL* 5.2 11.8 - - - +
160J TYR* 3.0 47.8 - - + +
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Residues in contact with HIS 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I ASN* 5.6 3.6 - - - -
70I TRP* 4.4 15.7 - + - -
71I GLU* 3.3 52.4 + - + +
73I ARG* 4.9 1.6 - - - -
74I ILE* 5.0 2.7 - - + -
73J ARG* 3.8 25.0 + - - +
100J ARG 4.0 10.1 - - - +
101J LEU* 2.9 15.7 + - + +
103J MET* 1.3 81.5 - - - +
105J ARG* 1.3 64.9 + - - +
107J GLU* 3.8 5.0 + - - +
108J LYS* 3.1 52.1 + - + +
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Residues in contact with ARG 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I ASN* 4.9 14.6 - - - +
70I TRP* 5.8 1.3 - - + -
101J LEU* 3.1 21.9 + - + +
102J TYR* 3.1 43.5 + - - +
104J HIS* 1.3 76.0 - - - +
106J ILE* 1.3 55.9 - - - +
108J LYS* 2.8 23.4 + - - -
109J ASP* 2.8 32.2 + - - +
110J TRP* 5.9 3.6 - - - +
139J ILE* 4.3 21.2 - - - +
149J PHE* 5.0 12.4 - - - -
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Residues in contact with ILE 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J TYR 3.4 15.7 - - - +
103J MET* 3.5 14.4 - - - +
105J ARG* 1.3 77.3 - - + +
107J GLU* 1.3 61.6 + - - +
108J LYS 3.3 0.3 + - - -
110J TRP* 3.4 23.8 + - + +
111J TYR* 3.2 36.0 + - + -
157J VAL* 5.6 2.5 - - + +
160J TYR* 3.4 44.2 - - + +
161J LEU* 3.4 31.6 - - + -
164J LEU* 4.2 2.2 - - + -
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Residues in contact with GLU 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 4.0 15.9 + - - +
24J GLN* 2.8 28.2 + - - +
73J ARG* 6.2 1.8 - - - +
103J MET* 3.1 20.9 + - + +
104J HIS* 4.4 5.4 - - - +
105J ARG 3.2 1.2 - - - -
106J ILE* 1.3 76.1 - - - +
108J LYS* 1.3 62.7 + - + +
111J TYR* 3.0 39.5 - - - +
112J THR* 4.1 7.3 + - - -
160J TYR* 3.1 34.6 - - + +
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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