Contacts of the helix formed by residues 100 - 114 (chain D) in PDB entry 4DHI
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 GLN 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B PRO* 4.9 10.9 - - - +
130B TRP* 3.7 21.3 - - - +
131B THR* 3.9 20.0 - - + +
7D ARG* 4.0 3.1 - - - +
11D GLU* 3.4 17.9 - - - +
14D ARG* 3.9 26.0 + - - +
62D TYR* 3.7 8.7 - - - -
95D TRP* 4.0 5.6 - - - -
98D ALA 5.0 0.8 + - - -
99D LEU* 1.3 77.7 - - - +
101D ILE* 1.3 69.9 + - - +
102D ARG* 3.9 18.2 + - + +
103D THR* 3.0 30.5 + - - +
104D VAL* 3.3 9.0 + - - +
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 2.9 29.7 + - + +
15D LEU* 3.8 26.5 - - + -
25D ALA* 5.8 0.4 - - + -
35D PHE* 4.1 22.0 - - + -
56D LEU* 4.1 20.4 - - + -
58D LEU* 3.8 42.4 - - + -
62D TYR* 3.6 4.9 + - - +
67D PRO* 4.6 4.7 - - + -
100D GLN* 1.3 70.6 - - - +
102D ARG* 1.3 64.2 + - - +
104D VAL* 3.0 11.6 + - - +
105D LEU* 2.9 36.1 + - + +
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Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 4.6 0.4 + - - -
14D ARG* 3.3 66.0 + - - +
15D LEU* 3.8 16.1 - - + +
18D GLU* 2.7 33.3 + - - +
19D PRO 4.1 2.0 + - - -
20D VAL* 3.8 28.3 - - + +
21D PRO* 5.8 0.4 - - - +
100D GLN* 3.2 16.6 + - + +
101D ILE* 1.3 79.8 - - - +
103D THR* 1.3 55.4 + - - +
105D LEU* 3.3 10.8 + - - +
106D LEU* 2.9 44.6 + - + +
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Residues in contact with THR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 4.1 17.7 - - + -
99D LEU* 3.9 25.5 - - + +
100D GLN* 3.0 32.6 + - - +
102D ARG* 1.3 78.7 - - - +
104D VAL* 1.3 58.4 + - - +
106D LEU* 3.5 8.6 + - - +
107D SER* 3.0 29.0 + - - -
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 4.5 8.1 - - + -
67D PRO* 4.3 10.1 - - + -
69D VAL* 4.1 12.6 - - + -
88D LEU* 5.4 1.1 - - + -
90D ILE* 4.3 13.9 - - + -
91D LEU* 3.9 30.3 - - + -
95D TRP* 3.8 23.3 - - + -
100D GLN 3.7 11.0 - - - +
101D ILE* 3.0 8.4 + - - +
103D THR* 1.3 74.1 - - - +
105D LEU* 1.3 66.9 + - + +
107D SER* 3.2 2.3 + - - -
108D ILE* 3.0 43.7 + - + +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.1 13.5 - - + -
20D VAL* 4.5 9.6 - - + -
23D ILE* 3.5 31.9 - - + +
25D ALA* 3.9 23.1 - - + -
37D VAL* 3.9 32.3 - - + -
39D ILE* 4.5 3.7 - - + +
54D LEU* 6.4 0.4 - - + -
56D LEU* 4.4 15.3 - - + -
69D VAL* 6.4 0.7 - - + -
101D ILE* 2.9 33.2 + - + +
102D ARG 3.8 4.5 - - - +
104D VAL* 1.3 79.5 - - + +
106D LEU* 1.3 63.3 + - - +
108D ILE* 3.4 10.0 + - + +
109D GLN 3.1 18.5 + - - -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 3.5 28.0 - - + -
21D PRO* 5.6 1.8 - - + -
23D ILE* 4.4 0.2 - - - +
102D ARG* 2.9 39.0 + - + +
103D THR* 3.8 7.2 - - - +
105D LEU* 1.3 76.8 - - - +
107D SER* 1.3 57.0 + - - +
109D GLN* 3.5 18.2 + - - +
110D ALA* 2.9 29.6 + - - +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 3.4 32.0 - - - +
90D ILE* 4.1 12.7 - - - +
103D THR* 3.0 19.1 + - - -
104D VAL 3.7 4.3 - - - -
106D LEU* 1.3 72.7 - - - +
108D ILE* 1.3 64.5 + - - +
110D ALA* 3.3 8.0 + - - +
111D LEU* 3.0 24.4 + - - +
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ILE* 3.7 20.0 - - + -
54D LEU* 4.2 5.4 - - + -
69D VAL* 4.0 12.3 - - + -
71D PHE* 3.9 28.9 - - + -
86D ILE* 3.5 27.4 - - + -
88D LEU* 4.0 14.1 - - + -
91D LEU* 5.0 1.1 - - + -
104D VAL* 3.0 37.7 + - + +
105D LEU* 3.9 10.3 - - + +
107D SER* 1.3 73.0 - - - +
109D GLN* 1.3 66.9 + - - +
111D LEU* 3.1 19.8 + - + +
112D LEU* 3.2 14.4 + - + +
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Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 4.2 0.6 - - - +
21D PRO 3.0 27.0 + - - +
22D GLY* 4.1 7.1 - - - +
23D ILE* 3.7 19.4 - - + +
39D ILE* 4.4 19.2 - - + +
40D ALA 5.2 2.1 - - - +
42D PRO* 4.0 15.4 - - + +
105D LEU 3.1 17.0 + - - +
106D LEU* 3.7 26.7 + - - +
108D ILE* 1.3 78.1 - - - +
110D ALA* 1.3 61.3 + - - +
112D LEU* 3.1 17.9 + - - +
113D SER* 3.4 8.7 + - - -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU 2.9 17.7 + - - +
107D SER* 3.6 8.5 - - - +
108D ILE 3.2 0.2 - - - -
109D GLN* 1.3 76.0 - - - +
111D LEU* 1.3 56.7 + - - +
113D SER* 3.1 9.3 + - - +
114D ALA* 3.0 30.2 + - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D HIS* 2.9 31.2 + - + +
79D ASN* 4.0 28.0 - - + +
80D VAL* 6.0 1.1 - - + -
86D ILE* 3.8 24.0 - - + -
87D CYS 4.4 0.2 - - - +
88D LEU* 3.8 33.0 - - + -
107D SER* 3.0 11.7 + - - +
108D ILE* 3.3 13.2 - - + +
110D ALA* 1.3 76.2 - - - +
112D LEU* 1.3 64.4 + - + +
114D ALA 4.1 11.2 - - - +
115D PRO* 3.1 17.3 - - - +
116D ASN* 4.8 7.2 - - + -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ILE* 3.9 30.3 - - + -
40D ALA 4.6 1.3 - - - +
41D GLY* 4.8 0.4 - - - -
42D PRO* 3.6 22.0 - - + -
45D SER* 3.5 9.9 - - - -
46D PRO* 4.5 0.5 - - - +
47D PHE* 3.5 26.9 - - + -
52D PHE* 4.6 16.6 - - + -
71D PHE* 4.2 17.3 - - + -
75D ILE* 3.4 29.2 - - + -
77D HIS* 3.9 15.3 - - + +
80D VAL* 5.6 1.3 - - + -
108D ILE* 3.6 13.5 - - + +
109D GLN 3.1 7.7 + - - +
111D LEU* 1.3 80.6 - - + +
113D SER* 1.3 59.1 + - - +
115D PRO* 4.0 4.9 - - - +
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PRO* 3.3 25.5 - - - +
43D GLN 5.1 1.7 + - - -
45D SER* 4.4 9.1 - - - -
46D PRO* 6.3 0.2 - - - -
109D GLN* 3.4 4.5 + - - +
110D ALA* 3.1 12.2 + - - -
112D LEU* 1.3 78.1 - - - +
114D ALA* 1.3 61.1 + - - +
115D PRO* 3.6 5.3 - - - +
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA 3.0 12.8 + - - +
111D LEU* 3.2 14.1 - - - +
113D SER* 1.3 81.6 - - - +
115D PRO* 1.3 68.9 - - - +
116D ASN* 3.2 6.9 + - - +
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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