Contacts of the helix formed by residues 90 - 108 (chain A) in PDB entry 3DNJ
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 THR 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.8 21.3 - - + +
89A TYR* 1.3 76.4 - - - +
91A TYR* 1.3 66.4 + - - +
92A GLU* 4.3 8.3 + - - +
93A VAL* 3.2 26.0 + - - +
94A ALA* 2.9 20.6 + - - +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.5 50.2 - + + -
89A TYR 3.8 0.6 + - - -
90A THR* 1.3 73.9 - - - +
92A GLU* 1.3 75.8 + - + +
94A ALA* 3.2 2.8 + - - +
95A GLU* 2.9 59.3 + - + +
116A MET* 3.5 23.0 - - + +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 3.3 8.6 + - - +
91A TYR* 1.3 95.0 + - + +
93A VAL* 1.3 59.5 + - + +
95A GLU* 3.5 19.6 + - - +
96A THR* 2.8 29.9 + - - -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.7 29.6 - - + -
90A THR* 3.2 22.0 + - - +
92A GLU* 1.3 78.0 - - + +
94A ALA* 1.3 65.0 + - - +
96A THR* 3.1 9.7 + - - -
97A LYS* 2.9 35.0 + - + +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.9 17.3 - - + +
43A VAL* 3.8 24.8 - - + +
89A TYR* 3.7 6.6 - - + +
90A THR 2.9 15.5 + - - +
91A TYR 3.5 4.9 - - - +
93A VAL* 1.3 77.1 - - - +
95A GLU* 1.3 61.8 + - - +
97A LYS* 3.2 2.6 + - - +
98A VAL* 3.0 27.5 + - - +
116A MET* 3.6 20.4 - - + -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 2.9 51.8 + - + +
92A GLU* 3.6 20.2 - - - +
93A VAL 3.2 0.4 - - - -
94A ALA* 1.3 76.3 - - - +
96A THR* 1.3 63.7 + - - +
98A VAL* 3.5 4.1 + - - +
99A ALA* 3.0 24.4 + - - +
116A MET* 3.7 16.8 - - - -
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLU 2.8 20.2 + - - -
93A VAL* 3.4 13.0 - - - -
95A GLU* 1.3 77.1 - - - +
97A LYS* 1.3 59.1 + - + +
99A ALA* 3.3 6.1 + - - +
100A GLN* 2.9 56.9 + - + +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.4 4.7 - - + -
63A PHE* 2.8 33.0 + - + +
64A PHE* 3.7 27.4 - - + +
65A ASN* 4.9 8.5 + - - -
89A TYR* 3.7 33.4 - - + -
93A VAL* 2.9 27.1 + - + +
94A ALA 3.7 6.1 - - - +
96A THR* 1.3 74.2 - - + +
98A VAL* 1.3 65.5 + - - +
100A GLN* 3.2 18.2 + - - +
101A VAL* 3.0 29.8 + - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.0 11.4 - - + -
94A ALA 3.0 21.1 + - - +
95A GLU* 3.8 5.6 - - - +
97A LYS* 1.3 74.1 - - - +
99A ALA* 1.3 64.4 + - - +
101A VAL* 3.2 3.6 + - - +
102A ILE* 3.0 35.2 + - + +
114A CYS* 3.5 32.5 - - - +
115A THR* 3.7 29.4 - - - +
116A MET* 4.2 14.1 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU 3.0 18.2 + - - +
96A THR* 3.6 6.5 - - - +
98A VAL* 1.3 79.7 - - - +
100A GLN* 1.3 57.7 + - + +
102A ILE* 3.3 7.2 + - - +
103A ASP* 2.9 31.6 + - - +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 3.6 35.4 - - + +
96A THR* 2.9 40.5 + - + +
97A LYS* 3.2 18.8 + - - +
99A ALA* 1.3 79.0 - - + +
101A VAL* 1.3 56.3 + - - +
103A ASP* 3.7 7.6 - - - +
104A SER* 3.0 30.0 + - - -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.7 2.2 - - + -
55A PHE* 5.4 0.3 - - - -
59A VAL* 3.8 15.7 - - + +
63A PHE* 4.4 10.1 - - + -
64A PHE* 3.6 33.2 - - + -
97A LYS 3.0 18.1 + - - +
98A VAL 3.6 6.3 - - - +
100A GLN* 1.3 73.7 - - - +
102A ILE* 1.3 61.8 + - - +
104A SER* 3.3 5.1 + - - -
105A ALA* 2.8 28.3 + - + +
112A LEU* 3.9 27.1 - - + +
114A CYS* 3.8 24.9 - - + -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 3.0 39.1 + - + +
99A ALA* 3.9 6.1 - - - +
101A VAL* 1.3 73.8 - - - +
103A ASP* 1.3 65.1 + - - +
105A ALA* 3.3 5.7 + - - +
106A ARG* 2.9 55.4 + - + +
112A LEU 4.8 1.6 - - - +
113A GLN* 5.8 2.7 - - - +
114A CYS* 3.9 23.8 - - + +
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 2.9 18.4 + - - +
100A GLN* 3.7 7.6 - - - +
102A ILE* 1.3 77.8 - - - +
104A SER* 1.3 62.6 + - - +
106A ARG* 4.1 2.3 - - - +
107A ARG* 2.9 64.6 + - - +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.5 15.8 - - - -
58A TYR* 3.9 11.8 + - - -
59A VAL* 5.3 0.2 - - - -
63A PHE* 3.8 21.1 - - - -
100A GLN 3.0 18.3 + - - -
101A VAL 3.8 2.9 - - - -
103A ASP* 1.3 77.8 - - - +
105A ALA* 1.3 63.8 + - - +
107A ARG* 3.4 15.4 + - - +
108A HIS* 2.7 42.4 + - - -
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.7 20.3 - - + -
101A VAL 2.8 21.9 + - - +
102A ILE 3.8 0.4 - - - +
104A SER* 1.3 73.6 - - - +
106A ARG* 1.3 81.8 + - - +
108A HIS* 3.1 9.2 + - - +
109A GLN 3.1 0.2 + - - -
110A HIS* 2.9 30.2 + - + +
112A LEU* 3.9 22.0 - - + +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 2.9 41.6 + - + +
103A ASP* 4.2 2.5 - - - +
105A ALA* 1.3 84.8 - - - +
107A ARG* 1.3 58.5 + - + +
109A GLN* 2.9 26.5 + - - +
110A HIS 3.0 24.8 + - - +
111A PRO* 3.2 10.7 - - - +
112A LEU 2.8 23.6 + - - +
113A GLN* 2.9 32.1 + - - +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 6.0 0.8 - - - -
103A ASP* 2.9 53.7 + - - +
104A SER* 3.7 19.0 + - - +
106A ARG* 1.3 77.2 - - + +
108A HIS* 1.3 70.4 + - - +
109A GLN* 3.1 17.0 + - - +
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Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.7 14.9 - + + -
58A TYR* 4.8 12.5 + + - -
104A SER* 2.7 43.8 + - - +
105A ALA 3.1 0.4 + - - +
107A ARG* 1.3 92.6 - - - +
109A GLN* 1.3 73.7 + - - +
110A HIS* 3.2 36.0 + - + +
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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