Contacts of the helix formed by residues 83 - 98 (chain A) in PDB entry 1DJ9
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 SER 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PHE* 4.4 7.3 - - - -
81A GLY 3.4 1.8 + - - -
82A TYR* 1.3 76.6 - - - +
84A VAL* 1.3 70.3 + - - +
85A VAL* 3.2 18.6 + - - +
86A HIS* 3.1 33.7 + - - +
87A GLN* 2.9 21.9 + - - +
270A PRO* 4.0 20.0 - - - +
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Residues in contact with VAL 84 (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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69A PHE* 4.8 11.4 - - + -
82A TYR 3.9 1.2 + - - +
83A SER* 1.3 76.5 + - - +
85A VAL* 1.3 67.3 + - + +
87A GLN* 3.5 20.0 + - - +
88A ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 85 (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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69A PHE* 3.5 36.8 - - + -
83A SER* 3.0 10.0 + - - +
84A VAL* 1.3 79.9 - - + +
86A HIS* 1.3 59.5 + - - +
88A ALA* 4.4 4.3 - - - +
89A LEU* 3.1 26.3 + - - +
270A PRO* 4.0 5.2 - - + +
273A ALA* 3.8 7.8 - - + +
274A GLN* 3.1 48.7 - - + +
277A ARG* 3.7 16.7 - - - +
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Residues in contact with HIS 86 (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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73A SER* 4.5 1.3 - - - -
81A GLY 3.4 19.3 + - - -
82A TYR* 4.0 15.2 - + + -
83A SER* 3.1 34.3 + - - +
85A VAL* 1.3 74.1 - - - +
87A GLN* 1.3 66.3 + - - +
89A LEU 3.3 0.7 + - - -
90A GLU* 3.1 29.7 + - - +
104A LEU* 3.7 20.5 - - + +
267A SER* 3.6 10.4 - - - -
268A MET* 2.9 50.0 + - + +
270A PRO* 4.1 10.9 - - + -
273A ALA* 3.7 14.8 - - + -
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Residues in contact with GLN 87 (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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82A TYR* 3.3 36.5 + - + +
83A SER 2.9 12.3 + - - +
84A VAL* 3.5 22.6 + - - +
86A HIS* 1.3 77.3 - - - +
88A ALA* 1.3 64.2 + - - +
90A GLU* 3.2 4.4 + - - +
91A GLU* 3.0 48.0 + - + +
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Residues in contact with ALA 88 (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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84A VAL 2.9 17.7 + - - +
85A VAL 3.8 2.2 - - - +
86A HIS 3.4 0.2 - - - -
87A GLN* 1.3 76.8 - - - +
89A LEU* 1.3 64.4 + - - +
91A GLU* 3.7 12.5 - - - +
92A GLU* 2.9 33.1 + - - +
277A ARG* 3.5 33.4 - - - +
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Residues in contact with LEU 89 (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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85A VAL 3.1 18.3 + - - +
86A HIS 3.7 5.4 - - - +
87A GLN 3.2 0.4 - - - -
88A ALA* 1.3 77.2 - - - +
90A GLU* 1.3 50.8 + - - +
92A GLU* 3.2 3.9 + - - +
93A LEU* 2.8 63.3 + - + +
104A LEU* 4.1 15.7 - - + -
234A PHE* 5.4 0.7 - - + -
238A PHE* 5.9 0.9 - - + -
273A ALA* 3.6 19.5 - - + +
276A LEU* 3.5 40.4 - - + +
277A ARG* 3.6 32.7 - - + +
280A LEU* 4.8 7.4 - - + -
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Residues in contact with GLU 90 (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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82A TYR* 2.8 37.9 + - - -
86A HIS 3.1 14.2 + - - +
87A GLN* 3.6 4.9 - - - +
89A LEU* 1.3 74.5 - - - +
91A GLU* 1.3 61.4 + - + +
93A LEU* 4.4 3.6 - - - -
94A ALA* 3.0 26.2 + - - +
101A ARG* 5.8 2.4 + - - -
102A ALA* 3.2 40.6 - - + +
103A LEU* 3.4 12.7 - - - +
104A LEU* 3.1 38.2 + - + +
262A LEU* 6.1 0.3 - - - +
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Residues in contact with GLU 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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87A GLN* 3.0 40.4 + - + +
88A ALA* 3.7 11.8 - - - +
90A GLU* 1.3 77.0 - - + +
92A GLU* 1.3 60.9 + - + +
94A ALA* 3.4 5.6 + - - +
95A GLU* 2.9 30.9 + - - +
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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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88A ALA* 2.9 22.1 + - - +
89A LEU* 3.6 3.6 - - - +
91A GLU* 1.3 77.4 - - + +
93A LEU* 1.3 59.2 + - - +
95A GLU* 3.4 7.1 + - - +
96A TRP* 2.8 30.7 + - - +
277A ARG* 2.9 53.9 + - - +
280A LEU* 4.0 16.6 - - + +
284A ARG* 4.0 7.3 + - - +
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Residues in contact with LEU 93 (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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89A LEU* 2.8 36.4 + - + +
90A GLU* 3.8 5.8 - - - +
92A GLU* 1.3 72.0 - - - +
94A ALA* 1.3 55.5 + - - +
96A TRP* 3.1 29.4 + - + +
97A LEU* 3.0 34.0 + - + +
102A ALA* 4.1 6.7 - - + -
104A LEU* 3.9 15.7 - - + -
232A VAL* 4.8 3.6 - - + -
234A PHE* 3.7 39.9 - - + -
238A PHE* 4.4 1.1 - - + -
244A ALA* 3.9 17.5 - - + -
246A LEU* 4.0 7.2 - - + -
280A LEU* 4.0 14.3 - - + +
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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
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90A GLU 3.0 19.5 + - - +
91A GLU* 3.8 5.8 - - - +
93A LEU* 1.3 72.1 - - - +
95A GLU* 1.3 65.3 + - - +
97A LEU 3.5 0.2 + - - -
98A GLY* 3.1 4.9 + - - -
99A TYR 3.0 42.7 + - - +
100A SER 4.2 3.4 - - - +
101A ARG* 3.7 26.7 - - - -
102A ALA 3.9 0.2 - - - +
246A LEU* 3.8 11.6 - - - +
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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 GLU 2.9 18.2 + - - +
92A GLU* 3.5 5.6 - - - +
94A ALA* 1.3 79.0 - - - +
96A TRP* 1.3 61.5 + - - +
97A LEU 3.4 0.2 + - - -
98A GLY* 3.7 7.5 + - - -
99A TYR 5.0 0.4 - - - -
217A ARG* 5.3 2.6 + - - -
284A ARG* 2.6 43.4 + - - -
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Residues in contact with TRP 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 18.1 + - - +
93A LEU* 3.1 13.4 + - + +
95A GLU* 1.3 84.7 + - - +
97A LEU* 1.3 90.9 + - + +
98A GLY 3.8 0.2 + - - -
209A THR* 3.6 21.1 - - - -
210A GLY* 4.1 1.6 - - - -
215A GLN* 2.6 26.3 + - + +
216A GLY 3.0 26.0 - - - -
217A ARG* 2.6 58.9 + - + +
221A TRP* 4.6 0.9 - - - -
232A VAL* 5.4 1.1 - - + -
238A PHE* 3.7 30.5 - + - -
280A LEU* 3.6 17.3 - - + -
283A ILE* 4.1 9.2 - - + -
284A ARG* 3.5 35.2 - - + +
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Residues in contact with LEU 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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93A LEU* 3.0 11.9 + - + +
96A TRP* 1.3 112.3 - - + +
98A GLY* 1.3 61.0 + - - +
99A TYR* 3.5 26.5 - - + -
209A THR* 5.2 0.2 - - - +
217A ARG* 3.0 39.0 - - + +
221A TRP* 4.0 16.8 - - + -
226A LYS* 5.5 1.2 - - - +
230A LEU* 4.3 10.3 - - + -
232A VAL* 4.0 16.8 - - + -
246A LEU* 3.6 33.4 - - + -
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Residues in contact with GLY 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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94A ALA 3.1 5.4 + - - -
95A GLU 3.7 5.5 + - - -
96A TRP 3.5 2.8 + - - -
97A LEU* 1.3 79.7 - - - +
99A TYR* 1.3 60.8 + - - +
221A TRP* 4.6 8.7 - - - -
226A LYS* 2.9 27.0 + - - +
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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