Contacts of the helix formed by residues 91 - 107 (chain B) in PDB entry 4DBW
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 ARG 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.4 1.4 - - - +
90B HIS* 1.3 77.3 - - - +
92B PRO* 1.3 75.4 - - + +
93B GLU* 3.3 23.1 + - - +
94B LEU* 2.9 28.4 + - + +
95B VAL* 3.5 4.2 + - - +
124B PRO* 3.5 29.1 - - + +
140B ASP* 2.8 43.2 + - - +
141B ILE 5.4 1.6 + - - -
142B VAL* 3.9 10.9 - - + +
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Residues in contact with PRO 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS 3.2 3.5 - - - +
91B ARG* 1.3 88.6 - - + -
93B GLU* 1.3 67.6 + - - +
95B VAL* 3.2 26.7 + - + +
96B ARG 4.3 2.1 + - - -
142B VAL* 4.8 2.9 - - + -
146B THR* 3.4 45.8 - - - +
150B ALA* 3.5 15.0 - - + +
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 3.5 26.1 - - - +
92B PRO* 1.3 84.8 - - - +
94B LEU* 1.3 75.2 + - + +
95B VAL 3.4 0.2 - - - -
97B PRO* 3.4 21.8 - - - +
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Residues in contact with LEU 94 (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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88B THR 3.8 22.7 - - - +
89B PHE* 4.0 24.2 - - + +
91B ARG* 2.9 22.0 + - + +
93B GLU* 1.3 98.5 - - + +
95B VAL* 1.3 65.2 + - - +
96B ARG 3.6 0.7 - - - -
97B PRO* 3.4 6.7 - - + +
98B ALA* 3.1 24.8 + - - +
124B PRO* 4.1 18.6 - - + -
125B GLY 5.8 0.7 - - - +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.9 21.0 - - + +
89B PHE 3.6 16.4 - - - +
90B HIS 3.8 9.4 - - - +
91B ARG 3.7 5.8 - - - +
92B PRO* 3.2 16.4 + - + +
94B LEU* 1.3 77.5 - - - +
96B ARG* 1.3 64.7 + - - +
98B ALA* 3.1 5.2 + - - +
99B LEU* 3.1 19.9 + - - +
114B TYR* 4.7 1.3 - - + -
147B THR* 4.2 5.8 - - + -
150B ALA* 3.7 28.5 - - + -
151B MET* 3.9 26.2 - - - +
154B CYS* 4.2 8.3 - - - -
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Residues in contact with ARG 96 (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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92B PRO 4.3 2.4 + - - +
95B VAL* 1.3 76.3 - - - +
97B PRO* 1.3 68.6 - - + +
99B LEU* 3.1 3.6 + - - +
100B GLU* 2.8 51.6 + - - +
150B ALA* 5.4 1.5 - - + +
153B LYS* 5.0 6.0 + - + +
154B CYS* 3.9 19.9 - - - +
157B ALA* 3.5 26.5 - - - +
159B LEU* 3.7 32.8 - - + +
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Residues in contact with PRO 97 (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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93B GLU 3.4 25.1 - - - +
94B LEU* 3.4 10.5 - - + +
96B ARG* 1.3 95.7 - - + +
98B ALA* 1.3 55.9 + - - +
100B GLU* 3.3 16.5 + - - +
101B ASN* 2.8 29.6 + - - +
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Residues in contact with ALA 98 (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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53B HIS* 5.8 3.3 + - + -
85B LEU* 3.7 20.6 - - + -
86B TRP 6.0 0.2 - - - +
89B PHE* 4.0 23.1 - - + -
94B LEU 3.1 19.8 + - - +
95B VAL 3.1 4.9 + - - +
97B PRO* 1.3 72.7 - - - +
99B LEU* 1.3 66.6 + - - +
101B ASN* 3.3 6.9 + - - +
102B SER* 3.0 25.3 + - - -
114B TYR* 3.7 3.8 - - - +
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Residues in contact with LEU 99 (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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95B VAL 3.1 8.7 + - - +
96B ARG 3.5 8.3 - - - +
98B ALA* 1.3 76.9 - - - +
100B GLU* 1.3 57.4 + - - +
102B SER* 3.1 5.0 + - - -
103B LEU* 2.9 44.5 + - + +
111B VAL* 4.0 19.1 - - + -
114B TYR* 3.4 48.3 + - + -
154B CYS* 3.6 27.8 - - + -
159B LEU* 3.5 37.9 - - + +
160B ALA* 4.2 3.4 - - + -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 2.8 50.3 + - - +
97B PRO* 3.6 18.4 - - - +
99B LEU* 1.3 78.3 - - - +
101B ASN* 1.3 56.7 + - - +
103B LEU* 3.4 10.0 + - + +
104B LYS* 3.0 26.7 + - - +
159B LEU* 4.0 19.3 - - + +
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Residues in contact with ASN 101 (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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53B HIS* 5.1 10.3 - - - +
97B PRO 2.8 16.9 + - - +
98B ALA* 3.7 7.2 - - - +
99B LEU 3.2 0.2 - - - -
100B GLU* 1.3 72.8 - - - +
102B SER* 1.3 62.1 + - - +
104B LYS* 3.2 17.9 + - - +
105B LYS* 2.9 56.0 + - - +
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Residues in contact with SER 102 (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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53B HIS* 4.2 12.7 + - - +
58B GLU* 2.8 36.8 + - - +
81B TYR* 5.3 1.5 + - - -
83B SER* 3.7 13.8 + - - -
98B ALA 3.0 15.9 + - - -
99B LEU* 3.1 15.5 + - - -
101B ASN* 1.3 75.6 - - - +
103B LEU* 1.3 62.9 - - - +
105B LYS* 3.5 4.4 + - - +
106B ALA* 3.1 25.5 + - - +
111B VAL* 5.7 0.9 - - - -
114B TYR* 4.6 5.1 + - - -
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Residues in contact with LEU 103 (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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81B TYR* 5.9 0.4 - - + -
99B LEU* 2.9 24.8 + - + +
100B GLU* 3.6 10.3 - - + +
101B ASN 3.2 0.2 - - - -
102B SER* 1.3 76.8 - - - +
104B LYS* 1.3 53.4 + - - +
106B ALA* 3.5 1.7 + - - -
107B GLN* 2.8 27.9 + - - -
108B LEU* 3.1 31.5 + - + +
109B ASP 3.5 18.6 - - - +
110B TYR 3.5 29.4 - - - +
111B VAL* 3.6 19.3 - - + +
159B LEU* 3.9 33.2 - - + +
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Residues in contact with LYS 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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100B GLU 3.0 14.8 + - - +
101B ASN* 3.2 21.7 + - - +
103B LEU* 1.3 73.5 - - - +
105B LYS* 1.3 67.7 - - + +
107B GLN* 3.1 27.8 + - - +
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Residues in contact with LYS 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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53B HIS* 4.6 16.4 - - - +
56B ASN* 5.6 3.4 + - - -
58B GLU* 3.9 28.7 - - + +
59B GLU* 3.2 55.4 + - + +
101B ASN* 2.9 44.1 + - - +
102B SER* 3.8 4.5 - - - +
104B LYS* 1.3 79.5 - - + +
106B ALA* 1.3 59.2 + - - +
107B GLN* 3.5 6.4 + - - +
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Residues in contact with ALA 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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58B GLU* 3.4 20.6 - - + +
59B GLU 5.4 0.4 - - - -
62B GLY* 3.4 21.5 - - - +
66B ARG* 3.5 4.4 + - - -
81B TYR* 4.1 15.0 - - + +
102B SER 3.1 17.5 + - - +
103B LEU* 4.2 2.5 - - - +
105B LYS* 1.3 75.4 - - - +
107B GLN* 1.3 71.6 + - - +
108B LEU* 3.7 26.0 - - + +
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Residues in contact with GLN 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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66B ARG* 3.2 43.2 + - - +
103B LEU 2.8 11.2 + - - -
104B LYS* 3.1 21.0 + - - +
105B LYS 4.1 5.8 - - - +
106B ALA* 1.3 82.4 - - - +
108B LEU* 1.3 62.6 + - - +
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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