Contacts of the helix formed by residues 103 - 115 (chain B) in PDB entry 3HCD
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 LEU 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B TYR* 3.4 29.4 - - + +
28B GLN* 3.7 28.5 - - - +
30B PHE* 3.5 29.8 - - + +
101B ASP* 3.2 7.3 + - - +
102B PHE* 1.3 92.7 - - + +
104B GLU* 1.3 64.6 + - - +
105B VAL* 3.9 20.6 - - + -
106B ASN* 3.3 13.3 + - - +
107B ARG* 3.3 18.1 + - - +
3002B SAH 3.2 18.2 - - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE 3.8 3.0 + - - -
103B LEU* 1.3 68.0 - - - +
105B VAL* 1.3 68.2 + - + +
106B ASN 3.0 2.7 - - - -
107B ARG* 3.0 33.7 + - + +
108B GLN* 2.8 47.6 + - + +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE 4.4 5.4 - - - +
32B PRO* 3.9 28.0 - - + +
103B LEU* 3.9 26.0 - - + -
104B GLU* 1.3 80.2 - - + +
106B ASN* 1.3 61.8 + - - +
108B GLN* 3.7 18.5 + - - +
109B GLU* 3.2 20.8 + - - +
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.5 17.0 - - - -
32B PRO* 3.3 23.8 - - - +
81B GLY* 3.8 19.4 - - - +
82B PRO* 3.4 24.1 - - - +
101B ASP* 2.8 30.9 - - - +
103B LEU* 3.3 6.1 + - - +
104B GLU 3.0 0.6 - - - -
105B VAL* 1.3 78.7 - - - +
107B ARG* 1.3 65.4 + - - +
109B GLU* 3.0 13.2 + - - +
110B LEU* 3.0 16.6 + - - +
3002B SAH 2.8 16.3 + - - -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASP* 3.0 30.9 + - + +
102B PHE 3.4 16.8 + - - -
103B LEU 3.3 10.3 - - - +
104B GLU* 3.0 38.7 + - + +
106B ASN* 1.3 77.0 - - - +
108B GLN* 1.3 50.5 + - + +
110B LEU* 3.3 8.0 + - - +
111B GLY* 2.7 31.5 + - - -
154B VAL* 3.7 30.9 + - + +
155B LEU 3.7 24.2 - - - -
156B PRO* 3.5 26.9 - - - +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU* 2.8 39.2 + - - +
105B VAL* 3.7 23.0 - - - +
107B ARG* 1.3 72.7 - - + +
109B GLU* 1.3 60.5 + - - +
111B GLY* 3.6 3.1 - - - +
112B ARG* 3.0 36.7 + - + +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 4.4 10.9 - - + +
33B ARG* 2.5 43.0 + - - +
36B LEU* 4.3 8.7 - - + -
82B PRO* 3.9 27.6 - - + +
105B VAL 3.2 11.7 + - - +
106B ASN* 3.0 10.8 + - - +
108B GLN* 1.3 77.2 - - - +
110B LEU* 1.3 65.2 + - - +
112B ARG* 3.1 32.7 + - - +
113B TRP* 3.2 12.0 + - - +
120B ALA* 4.3 3.1 - - - +
121B PHE* 3.9 11.3 + - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B SER* 4.1 7.6 - - - -
81B GLY 3.3 28.7 - - - +
82B PRO 3.8 11.4 - - - +
83B THR 3.7 19.3 - - - +
84B VAL* 4.1 11.4 - - + -
99B MET* 3.8 30.5 - - + -
100B THR 5.1 3.1 - - - +
101B ASP* 5.6 0.2 - - + -
106B ASN 3.0 12.0 + - - +
107B ARG* 3.4 8.1 - - + +
109B GLU* 1.3 75.1 - - - +
111B GLY* 1.3 58.1 + - - +
113B TRP* 2.9 8.2 + - + +
114B LEU* 2.8 35.4 + - + +
154B VAL* 4.1 29.4 - - + -
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG 2.7 18.7 + - - -
108B GLN* 3.6 6.1 - - - -
109B GLU 3.2 0.6 - - - -
110B LEU* 1.3 73.1 - - - +
112B ARG* 1.3 60.1 + - - +
114B LEU* 3.6 12.1 + - - +
115B GLN* 2.8 39.1 + - - +
154B VAL* 5.6 0.9 - - - +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 4.0 9.3 - - - +
108B GLN* 3.0 21.8 + - - +
109B GLU* 3.4 28.8 + - - +
110B LEU 3.1 0.4 - - - -
111B GLY* 1.3 77.6 - - - +
113B TRP* 1.3 63.4 + - - +
115B GLN* 3.6 4.5 + - - +
116B GLU 3.4 1.7 + - - -
117B GLU* 3.2 50.0 + - - +
119B GLY* 2.9 43.5 + - - -
120B ALA* 3.5 13.5 - - + +
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.9 29.8 - - + -
88B LEU* 5.8 0.7 - - + -
99B MET* 6.2 1.3 - - - -
109B GLU 3.2 9.6 + - - +
110B LEU* 2.9 10.6 + - + +
112B ARG* 1.3 75.4 - - - +
114B LEU* 1.3 77.9 + - + +
116B GLU* 2.8 17.2 + - - +
120B ALA* 3.7 10.3 - - + +
121B PHE* 3.5 25.1 + - + +
123B TRP* 3.6 27.7 - + + +
127B SER* 5.5 0.4 - - - -
144B GLU* 4.0 29.6 + - + -
147B LEU* 3.8 31.4 - - + -
148B ARG* 2.9 66.4 + - + +
151B VAL* 5.6 1.6 - - + -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 5.7 2.9 - - - -
110B LEU* 2.8 24.2 + - + +
111B GLY* 3.7 11.9 - - - +
113B TRP* 1.3 88.4 - - + +
115B GLN* 1.3 58.3 + - + +
116B GLU* 3.3 3.5 + - - +
148B ARG* 3.7 44.2 + - + +
151B VAL* 4.0 28.7 - - + +
154B VAL* 3.9 27.8 - - + -
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLY* 2.8 33.4 + - - +
112B ARG* 4.0 2.4 - - - +
113B TRP 3.2 0.4 - - - -
114B LEU* 1.3 75.4 - - + +
116B GLU* 1.3 69.6 + - - +
117B GLU* 3.1 36.8 + - + +
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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