Contacts of the helix formed by residues 102 - 116 (chain B) in PDB entry 5A72
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 LYS 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B VAL 3.8 10.1 - - - +
21B ASP* 3.0 43.4 + - - +
22B ALA 5.0 3.0 + - - -
24B GLY 3.1 23.9 + - - +
25B CYS* 4.3 0.2 - - - +
26B ILE* 3.9 31.5 - - + +
99B LEU* 4.5 5.8 - - + -
100B ASN 3.4 0.2 - - - -
101B LEU* 1.3 80.8 - - + +
103B ARG* 1.3 63.7 + - - +
104B ALA 3.1 3.3 + - - -
105B GLN* 3.3 28.7 + - - +
106B ALA* 3.0 22.9 + - - +
615D G 4.6 2.6 + - - -
616D A 3.4 18.6 + - - -
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Residues in contact with ARG 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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96B LEU* 3.2 30.5 + - + +
97B PRO* 3.2 25.6 + - - +
98B TYR 4.3 0.8 - - - -
99B LEU* 2.8 37.2 + - + +
100B ASN* 3.8 15.1 + - - +
101B LEU 3.4 2.8 - - - -
102B LYS* 1.3 75.4 - - - +
104B ALA* 1.3 66.4 + - - +
106B ALA* 4.4 3.8 - - - -
107B LYS* 2.9 30.7 + - + +
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Residues in contact with ALA 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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101B LEU 4.6 3.3 + - - +
102B LYS 3.1 0.6 - - - -
103B ARG* 1.3 79.6 - - - +
105B GLN* 1.3 67.8 + - - +
107B LYS* 3.3 4.2 + - - +
108B LEU* 2.9 27.1 + - + +
138B LEU* 3.6 27.1 - - + -
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Residues in contact with GLN 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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26B ILE* 3.5 33.4 + - + +
101B LEU 3.7 6.3 + - - +
102B LYS* 3.3 48.8 + - - +
104B ALA* 1.3 77.7 - - - +
106B ALA* 1.3 58.4 + - - +
108B LEU* 3.3 4.5 + - - +
109B VAL* 2.8 34.3 + - - +
135B VAL* 3.9 18.4 - - + +
138B LEU* 3.9 36.1 + - + +
139B THR* 4.5 8.2 - - + +
616D A 5.5 0.6 + - - -
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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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26B ILE* 4.0 16.1 - - + +
92B LEU* 4.1 13.3 - - + +
96B LEU* 3.5 24.9 - - + -
99B LEU* 3.9 14.4 - - + -
102B LYS 3.0 17.1 + - - +
103B ARG 3.9 0.9 - - - +
105B GLN* 1.3 77.3 - - - +
107B LYS* 1.3 58.4 + - - +
109B VAL* 3.7 1.6 - - - +
110B LEU* 2.9 34.4 + - - +
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Residues in contact with LYS 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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96B LEU* 3.9 28.8 - - + +
103B ARG* 2.9 24.5 + - + +
104B ALA* 3.8 4.0 - - - +
106B ALA* 1.3 75.4 - - - +
108B LEU* 1.3 64.6 + - + +
110B LEU* 3.2 17.2 + - + +
111B GLN* 3.1 41.4 + - - +
114B LYS* 5.6 3.4 - - - +
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Residues in contact with LEU 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 ALA* 2.9 18.0 + - + +
105B GLN 3.7 3.8 - - - +
107B LYS* 1.3 79.1 - - + +
109B VAL* 1.3 57.5 + - - +
111B GLN* 2.9 28.0 + - + +
112B ILE* 3.1 16.3 + - - +
131B LEU* 4.2 22.3 - - + +
134B LYS* 3.9 29.8 - - + -
135B VAL* 3.8 23.6 - - + -
138B LEU* 4.0 22.0 - - + -
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Residues in contact with VAL 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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26B ILE* 4.0 11.9 - - + -
27B ASN* 3.7 24.7 - - - +
28B ALA* 4.3 9.0 - - + -
44B VAL* 3.8 26.2 - - + -
88B LEU* 4.0 8.3 - - + -
92B LEU* 3.9 21.5 - - + -
105B GLN 2.8 24.8 + - - +
106B ALA 3.7 3.1 - - - +
108B LEU* 1.3 72.9 - - - +
110B LEU* 1.3 63.5 + - - +
112B ILE* 3.1 9.8 + - - +
113B ILE* 2.9 24.5 + - + +
135B VAL* 4.4 7.0 - - + -
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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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89B GLN* 4.1 32.1 - - + +
92B LEU* 4.1 26.9 - - + -
93B GLU* 4.8 10.3 - - + +
96B LEU* 3.6 31.2 - - + -
106B ALA 2.9 19.1 + - - +
107B LYS* 3.4 22.2 - - + +
109B VAL* 1.3 77.7 - - - +
111B GLN* 1.3 63.7 + - - +
113B ILE* 3.3 10.2 + - + +
114B LYS* 3.3 27.0 + - - +
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Residues in contact with GLN 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 LYS* 3.1 33.3 + - - +
108B LEU* 2.9 20.5 + - + +
110B LEU* 1.3 73.9 - - - +
112B ILE* 1.3 67.2 + - - +
114B LYS* 3.1 52.8 + - - +
115B LYS* 3.6 11.9 - - - +
131B LEU* 3.7 20.0 - - + -
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Residues in contact with ILE 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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28B ALA* 3.6 31.0 - - + -
42B VAL* 3.8 16.8 - - + -
44B VAL* 3.7 20.0 - - + -
108B LEU 3.1 11.9 + - - +
109B VAL* 3.1 11.0 + - - +
111B GLN* 1.3 75.1 - - - +
113B ILE* 1.3 58.7 + - - +
115B LYS* 2.9 24.0 + - - +
116B LEU* 3.2 22.2 + - + +
128B ALA* 4.1 9.2 - - + +
131B LEU* 3.6 25.8 - - + +
132B ALA* 3.8 21.1 - - - +
135B VAL* 4.6 2.2 - - + -
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Residues in contact with ILE 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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44B VAL* 4.2 17.5 - - + -
85B GLY* 4.0 26.9 - - - +
88B LEU* 4.1 13.5 - - + -
89B GLN* 3.8 48.7 - - + +
109B VAL* 2.9 28.3 + - + +
110B LEU* 3.6 16.6 - - + +
111B GLN 3.2 0.2 - - - -
112B ILE* 1.3 78.2 - - - +
114B LYS* 1.3 63.1 + - - +
115B LYS 3.2 0.5 + - - -
116B LEU* 3.5 8.6 + - + +
117B PRO* 3.5 16.6 - - - +
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Residues in contact with LYS 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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107B LYS* 5.6 4.0 - - - +
110B LEU* 3.3 16.1 + - - +
111B GLN* 3.1 47.5 + - - +
113B ILE* 1.3 79.7 - - - +
115B LYS* 1.3 60.1 + - + +
117B PRO* 3.5 10.2 - - - +
118B ASN* 4.4 7.3 + - - -
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Residues in contact with LYS 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 GLN* 3.6 13.7 - - - +
112B ILE 2.9 8.0 + - - +
114B LYS* 1.3 78.1 - - + +
116B LEU* 1.3 57.7 + - - +
117B PRO* 3.2 4.5 - - - -
118B ASN* 2.8 25.1 + - - +
119B THR* 3.6 2.6 + - - +
124B VAL* 3.5 24.5 - - + +
127B GLU* 2.7 37.5 + - + +
128B ALA* 3.8 30.1 - - + +
131B LEU* 4.3 18.4 - - + -
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Residues in contact with LEU 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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41B GLN* 6.4 0.2 - - + -
42B VAL* 3.9 27.6 - - + +
44B VAL* 4.1 26.0 - - + -
85B GLY* 4.4 14.4 - - - +
112B ILE* 3.2 25.7 + - + +
113B ILE* 3.5 14.8 + - + +
115B LYS* 1.3 75.7 - - - +
117B PRO* 1.3 68.2 - - + +
118B ASN 3.1 0.7 + - - -
119B THR* 3.1 36.0 + - + +
128B ALA* 4.8 1.6 - - + -
503C A 4.7 8.0 + - - -
504C G 6.0 0.9 - - - +
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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