Contacts of the helix formed by residues 104 - 119 (chain B) in PDB entry 2I91
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 ASP 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.1 15.0 - - + +
68B GLY* 5.3 5.8 - - - +
70B GLY* 4.7 2.2 - - - -
71B CYS* 5.0 0.7 - - - -
102B CYS* 3.2 18.6 - - - +
103B SER* 1.3 83.7 + - - +
105B ILE* 1.3 66.3 + - - +
106B LYS* 3.1 23.9 - - - +
107B THR* 2.8 30.3 + - - +
108B LYS* 3.6 13.0 + - - +
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Residues in contact with ILE 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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537A LEU* 3.1 49.6 - - + -
103B SER 4.4 5.2 - - - +
104B ASP* 1.3 77.9 - - - +
106B LYS* 1.3 66.5 + - + +
107B THR 3.3 1.1 - - - -
108B LYS* 3.8 26.5 - - + +
109B GLN* 3.0 33.9 + - - +
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Residues in contact with LYS 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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532A ASN* 3.7 28.9 - - - +
537A LEU* 4.6 24.5 + - + +
71B CYS* 3.9 20.3 - - - -
104B ASP* 3.1 16.4 - - - +
105B ILE* 1.3 85.0 - - + +
107B THR* 1.3 56.8 + - - +
109B GLN* 3.5 20.4 + - - +
110B ALA* 3.0 29.1 + - - +
113B ARG* 4.6 4.3 + - - +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.9 1.6 - - + -
70B GLY* 2.8 42.5 - - - +
71B CYS* 3.6 8.0 + - - -
74B VAL* 4.1 2.3 - - + +
99B CYS* 3.9 22.2 - - + -
102B CYS* 3.5 27.5 - - - -
104B ASP* 2.8 21.9 + - - +
106B LYS* 1.3 75.8 - - - +
108B LYS* 1.3 59.3 + - - +
110B ALA* 3.1 3.7 + - - +
111B ALA* 2.8 27.5 + - - +
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Residues in contact with LYS 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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99B CYS 3.5 10.1 - - - +
100B SER 3.4 32.5 - - - +
101B GLN* 3.7 9.3 + - - +
102B CYS 3.6 21.4 + - - +
103B SER 4.5 4.3 + - - -
104B ASP 3.6 12.4 + - - +
105B ILE* 3.9 24.6 - - + +
106B LYS 3.4 0.4 - - - -
107B THR* 1.3 77.9 - - - +
109B GLN* 1.3 64.5 + - - +
111B ALA* 3.0 13.5 + - - +
112B PHE* 3.2 29.3 + - + -
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ASP* 2.6 38.8 + - - +
531A ARG* 4.6 10.3 + - - +
532A ASN* 3.5 22.2 + - - +
537A LEU* 5.4 1.7 - - - +
105B ILE 3.0 21.7 + - - +
106B LYS* 3.8 18.1 - - - +
108B LYS* 1.3 77.0 - - - +
110B ALA* 1.3 58.8 + - - +
112B PHE* 4.5 5.5 - - - +
113B ARG* 3.2 38.3 + - - +
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Residues in contact with ALA 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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71B CYS* 4.2 15.3 - - + -
74B VAL* 3.6 23.4 - - + +
106B LYS 3.0 17.9 + - - +
107B THR* 3.4 7.0 - - - +
108B LYS 3.1 0.4 - - - -
109B GLN* 1.3 77.4 - - - +
111B ALA* 1.3 63.4 + - - +
113B ARG* 3.4 33.4 + - - +
114B ALA* 3.2 17.7 + - - +
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Residues in contact with ALA 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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74B VAL* 4.2 9.8 - - + +
96B LEU* 3.5 22.0 - - + +
99B CYS* 4.0 8.1 - - + -
100B SER* 3.8 30.7 - - - +
107B THR 2.8 12.8 + - - +
108B LYS 3.0 9.4 + - - +
110B ALA* 1.3 77.1 - - - +
112B PHE* 1.3 62.4 + - - +
114B ALA* 3.2 12.3 + - - +
115B VAL* 3.3 13.0 + - - +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B SER* 3.5 43.7 - - - -
108B LYS* 3.2 35.4 + - + +
109B GLN* 4.6 4.7 - - - +
111B ALA* 1.3 76.1 - - + +
113B ARG* 1.3 62.0 + - - +
115B VAL* 3.4 26.4 + - + +
116B PRO* 4.0 3.6 - - - +
128B PHE* 4.5 5.8 - + - -
132B LYS* 4.3 13.5 - - - -
147B ALA* 3.6 32.1 - - + +
148B LEU* 4.1 21.1 - - + -
151B ALA* 3.9 29.3 - - + +
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Residues in contact with ARG 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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83A GLU* 4.6 21.9 + - - +
528A ASP* 5.2 2.8 + - - -
71B CYS* 5.6 2.6 - - - -
74B VAL* 6.0 0.6 - - - +
78B LYS* 6.5 1.1 - - - +
106B LYS* 4.6 5.1 + - - +
109B GLN* 3.2 34.1 + - - +
110B ALA* 3.4 40.6 + - - +
111B ALA 3.1 0.2 - - - -
112B PHE* 1.3 78.8 - - - +
114B ALA* 1.3 59.8 - - - +
116B PRO* 3.6 14.4 - - - +
117B GLU* 4.9 4.2 - - - +
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Residues in contact with ALA 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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74B VAL* 4.1 11.9 - - + -
78B LYS* 3.6 39.3 - - + +
96B LEU* 4.7 2.9 - - + -
110B ALA 3.2 14.5 + - - +
111B ALA 3.2 6.0 + - - +
113B ARG* 1.3 77.0 - - - +
115B VAL* 1.3 61.8 + - - +
116B PRO* 3.4 3.1 - - - -
117B GLU* 3.1 6.9 + - - +
118B VAL* 3.1 28.7 + - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.9 17.0 - - + -
111B ALA 3.3 15.6 + - - +
112B PHE* 3.4 18.6 - - + +
114B ALA* 1.3 76.0 - - - +
116B PRO* 1.3 61.5 - - + +
118B VAL* 4.7 2.2 - - - -
119B CYS* 2.7 57.7 + - + +
125B LEU* 4.6 13.5 - - + -
128B PHE* 4.0 18.6 - - + -
151B ALA* 4.6 20.4 - - + +
155B TRP* 4.7 6.7 - - + -
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Residues in contact with PRO 116 (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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112B PHE 4.0 4.3 - - - +
113B ARG 3.6 13.9 - - - +
114B ALA 3.4 2.9 - - - -
115B VAL* 1.3 97.0 - - + +
117B GLU* 1.3 66.7 + - + +
118B VAL 3.3 0.2 - - - -
119B CYS 3.8 11.1 - - - +
120B ARG* 4.6 5.5 + - - +
151B ALA* 5.8 2.9 - - + +
154B ASP* 5.6 5.2 - - + +
155B TRP* 4.2 28.2 + - + +
158B THR* 5.5 5.6 - - - +
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Residues in contact with GLU 117 (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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82A GLN* 3.4 22.1 - - - +
117A GLU* 4.7 0.7 - - - +
78B LYS* 2.9 31.7 + - + -
82B GLN* 2.8 47.7 + - - +
113B ARG 4.9 4.9 - - - +
114B ALA* 3.1 8.8 + - - +
116B PRO* 1.3 85.6 - - + +
118B VAL* 1.3 60.6 + - - +
120B ARG* 2.8 25.1 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.7 5.2 - - + -
78B LYS* 4.0 32.3 - - + +
81B SER* 3.8 23.7 + - - +
89B GLN* 4.8 1.4 - - - +
92B THR* 5.4 4.3 - - - -
93B LEU* 3.9 20.5 - - + +
96B LEU* 3.8 29.2 - - + -
114B ALA* 3.1 16.9 + - + +
115B VAL 4.0 1.8 - - - +
117B GLU* 1.3 83.3 - - - +
119B CYS* 1.3 60.2 + - - +
120B ARG* 3.5 11.1 + - - +
124B HIS* 3.7 11.8 + - - -
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Residues in contact with CYS 119 (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 LEU* 3.9 14.4 - - - -
96B LEU* 5.9 1.6 - - - -
115B VAL* 2.7 36.5 + - + +
116B PRO 3.8 6.4 - - - +
118B VAL* 1.3 75.2 - - - +
120B ARG* 1.3 59.5 + - - +
121B ILE 3.4 2.2 - - - -
124B HIS* 3.5 31.0 - - + -
125B LEU* 4.0 15.3 - - + +
128B PHE* 4.3 11.0 - - - -
155B TRP* 2.6 39.8 + - + +
159B LYS* 5.7 0.2 - - - -
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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
------------------------------------------------------------
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