Contacts of the helix formed by residues 99 - 112 (chain B) in PDB entry 3RU0
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 PRO 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TYR 4.5 0.9 - - - +
98B PRO* 1.3 92.9 - - + +
100B ASP* 1.3 66.9 + - - +
101B SER* 4.0 4.9 - - - +
102B VAL* 3.1 21.1 + - + +
103B ARG* 3.2 9.0 + - - +
147B LEU* 3.9 24.5 - - + -
150B THR* 3.7 20.4 - - + +
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Residues in contact with ASP 100 (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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39B THR* 3.9 4.8 - - + +
40B VAL 4.2 3.6 - - - +
41B CYS* 3.4 20.4 - - - +
42B LYS* 2.9 42.3 + - - +
97B TYR* 4.4 9.5 + - - -
98B PRO 4.5 0.8 - - - +
99B PRO* 1.3 71.7 - - - +
101B SER* 1.3 57.9 + - - +
103B ARG* 3.2 8.6 + - - +
104B LEU* 2.8 31.5 + - - +
195B VAL* 4.0 18.7 - - + +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PRO* 4.0 4.0 - - - +
100B ASP* 1.3 78.8 - - - +
102B VAL* 1.3 58.2 + - - +
104B LEU* 3.7 8.2 - - - +
105B LEU* 3.0 34.1 + - - +
147B LEU* 3.4 28.9 - - - +
175B PHE* 3.5 12.8 - - - -
178B VAL* 4.0 24.7 - - - -
179B ILE* 6.0 3.1 - - - -
195B VAL* 5.7 0.7 - - - -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.8 12.1 - - + -
99B PRO* 3.1 12.6 + - + +
101B SER* 1.3 75.6 + - - +
103B ARG* 1.3 65.1 + - - +
105B LEU* 3.9 0.7 - - - -
106B GLY* 3.0 21.3 + - - -
147B LEU* 3.8 31.0 - - + +
150B THR* 3.9 18.2 - - + -
151B PHE* 3.8 23.2 - - + +
154B PHE* 3.6 28.1 - - + -
175B PHE* 3.8 16.8 - - + -
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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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39B THR* 3.3 28.0 + - + +
40B VAL* 3.9 10.0 - - - +
45B ARG* 4.9 3.0 - - - +
50B ASP* 2.8 29.4 + - - -
67B VAL* 5.2 2.2 + - - +
68B ALA* 4.3 5.3 - - - +
86B GLU* 2.8 41.7 + - - +
90B LEU* 3.7 22.6 - - - +
97B TYR* 2.9 37.8 + - + +
98B PRO* 4.4 6.8 - - + +
99B PRO 3.2 11.9 + - - +
100B ASP* 3.7 8.7 - - - +
102B VAL* 1.3 78.4 - - - +
104B LEU* 1.3 60.7 + - - +
106B GLY* 3.5 1.6 + - - -
107B ARG* 3.2 28.8 + - - +
154B PHE* 4.3 16.1 - - + -
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Residues in contact with LEU 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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37B ALA* 3.4 35.9 - - + +
38B TYR* 3.8 10.8 - - - +
39B THR* 4.2 11.1 - - + +
100B ASP 2.8 16.9 + - - +
101B SER* 3.7 4.0 - - - +
103B ARG* 1.3 78.0 - - - +
105B LEU* 1.3 58.1 + - - +
107B ARG* 3.0 10.3 + - - +
108B VAL* 2.9 29.9 + - + +
178B VAL* 4.2 24.0 - - + -
195B VAL* 4.0 26.9 - - + +
196B GLY* 4.1 2.7 - - - -
197B LEU* 4.0 30.3 - - + +
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Residues in contact with LEU 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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101B SER 3.0 16.0 + - - +
102B VAL 4.1 0.9 - - - +
104B LEU* 1.3 71.8 - - - +
106B GLY* 1.3 65.5 + - - +
108B VAL* 3.5 21.7 - - + +
109B VAL* 3.0 31.5 + - + +
126B PHE* 4.2 10.3 - - + -
151B PHE* 3.8 14.4 - - + -
169B PHE* 4.7 3.6 - - + -
171B LEU* 4.8 2.2 - - + -
174B ALA* 3.8 20.4 - - + -
175B PHE* 3.5 57.0 - - + +
178B VAL* 3.7 22.2 - - + -
197B LEU* 5.0 0.4 - - + -
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Residues in contact with GLY 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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86B GLU* 6.0 5.4 - - - -
102B VAL 3.0 14.8 + - - -
103B ARG 3.7 4.9 - - - -
104B LEU 3.3 0.2 - - - -
105B LEU* 1.3 76.5 - - - +
107B ARG* 1.3 59.5 + - - +
109B VAL* 3.4 6.3 - - - +
110B PHE* 3.4 26.2 - - - -
151B PHE* 3.5 13.6 - - - -
154B PHE* 5.0 2.5 - - - -
155B MET* 3.9 18.7 - - - +
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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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37B ALA* 4.0 13.2 - - + +
38B TYR* 2.9 42.5 + - - +
39B THR* 4.7 7.4 - - - +
50B ASP* 4.5 11.3 + - - +
70B TYR* 5.5 1.0 + - - -
79B ALA* 5.5 3.2 + - - +
82B ASP* 3.7 50.7 + - + +
83B HIS* 4.5 5.1 + - - +
86B GLU* 2.7 43.5 + - + +
103B ARG* 3.2 24.7 + - - +
104B LEU* 3.0 9.4 + - - +
106B GLY* 1.3 75.9 - - - +
108B VAL* 1.3 64.4 + - - +
109B VAL 3.4 0.3 + - - -
110B PHE* 3.5 6.7 + - - +
111B LYS* 3.3 19.8 + - - +
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Residues in contact with VAL 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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36B LEU* 4.5 7.0 - - + -
37B ALA* 3.7 17.2 - - + +
104B LEU* 2.9 21.9 + - + +
105B LEU* 3.2 19.7 + - + +
107B ARG* 1.3 75.9 - - - +
109B VAL* 1.3 58.0 - - - +
111B LYS* 2.9 9.2 + - - +
112B LEU* 2.9 50.4 + - + +
126B PHE* 3.9 23.3 - - + -
169B PHE* 4.6 2.0 - - + -
197B LEU* 3.9 23.3 - - + -
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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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105B LEU 3.0 19.3 + - - +
106B GLY* 3.4 19.1 - - - +
108B VAL* 1.3 75.2 - - - +
110B PHE* 1.3 75.5 + - + +
112B LEU* 3.6 16.9 + - - +
113B MET* 3.5 19.5 - - - +
151B PHE* 3.9 12.6 - - + -
159B ILE* 4.0 7.4 - - + -
165B LEU* 3.8 25.1 - - + -
166B PRO* 4.3 3.4 - - + +
169B PHE* 3.3 40.8 - - + -
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Residues in contact with PHE 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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85B ARG* 3.4 72.5 - - + -
106B GLY 3.4 17.5 - - - -
107B ARG* 3.5 5.5 + - - +
108B VAL 3.2 0.4 - - - -
109B VAL* 1.3 75.9 - - + +
111B LYS* 1.3 65.7 + - - +
112B LEU 3.2 0.4 - - - -
113B MET* 3.2 40.4 + - + +
114B ASP* 3.8 5.0 + - - +
155B MET* 3.5 24.7 - - + -
158B GLU* 4.2 2.9 - - + -
159B ILE* 3.6 32.1 - - + -
164B GLN 5.7 0.2 - - - -
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Residues in contact with LYS 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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35B PRO 4.6 6.1 + - - -
36B LEU* 3.2 50.3 + - + +
37B ALA* 5.2 0.7 - - + -
82B ASP* 5.0 13.2 + - - +
107B ARG 3.3 13.7 + - - +
108B VAL* 2.9 13.6 + - - +
110B PHE* 1.3 78.8 - - - +
112B LEU* 1.3 60.6 + - - +
114B ASP* 3.2 26.8 + - + +
118B SER* 4.3 13.6 + - - -
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Residues in contact with LEU 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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36B LEU* 4.5 9.2 - - + -
108B VAL* 2.9 32.3 + - + +
109B VAL* 3.8 9.6 - - - +
110B PHE 3.2 0.4 - - - -
111B LYS* 1.3 77.9 - - - +
113B MET* 1.3 59.0 + - - +
114B ASP 3.3 6.0 + - - +
121B GLU* 4.4 9.6 - - - +
126B PHE* 3.7 33.0 - - + -
127B TYR* 3.6 31.5 + - + +
166B PRO* 4.6 8.0 - - + +
169B PHE* 3.6 33.2 - - + -
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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
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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