Contacts of the helix formed by residues 88 - 107 (chain B) in PDB entry 3LOC
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 ALA 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP 3.8 0.8 + - - -
87B PHE* 1.3 70.4 - - - +
89B PRO* 1.3 66.3 - - + +
90B LEU 3.4 1.1 - - - -
91B ALA* 3.3 19.0 + - + +
92B ALA* 2.9 27.7 + - - +
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Residues in contact with PRO 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE 3.3 6.7 - - - +
88B ALA* 1.3 82.6 - - + +
90B LEU* 1.3 66.5 + - + +
92B ALA* 3.1 6.2 + - + +
93B ILE* 2.9 30.8 + - + +
147B TRP* 3.6 46.7 - - + +
152B LYS* 3.7 37.0 - - + +
153B LEU* 4.2 13.7 - - + -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 5.1 0.2 - - - +
89B PRO* 1.3 77.8 - - + +
91B ALA* 1.3 64.6 + - - +
93B ILE* 3.2 1.7 + - - -
94B LYS* 3.0 31.0 + - - +
152B LYS 4.5 4.7 - - - +
153B LEU* 3.4 28.3 - - + -
205B ILE* 3.6 31.8 - - + +
208B ILE* 4.0 16.4 - - + +
209B ARG* 3.4 43.1 - - + +
210B PRO* 4.3 9.2 - - + -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 3.3 22.8 + - + +
89B PRO 3.2 0.4 - - - -
90B LEU* 1.3 80.4 - - - +
92B ALA* 1.3 62.4 + - - +
94B LYS* 3.3 13.6 + - + +
95B GLU* 3.2 23.6 + - - +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 4.0 27.3 - - + -
87B PHE* 4.3 22.9 - - + -
88B ALA 2.9 17.1 + - - +
89B PRO* 3.5 9.6 - - + +
91B ALA* 1.3 72.9 - - - +
93B ILE* 1.3 58.2 + - - +
95B GLU* 3.3 6.8 + - - +
96B TYR* 3.0 27.7 + - - +
147B TRP* 6.1 1.3 - - + +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 4.5 16.8 - - + -
89B PRO* 2.9 24.6 + - + +
90B LEU 3.2 4.5 + - - +
92B ALA* 1.3 73.8 - - - +
94B LYS* 1.3 66.7 + - - +
96B TYR* 3.3 6.4 + - - +
97B ILE* 2.9 35.7 + - + +
144B ILE* 5.9 3.4 - - + -
147B TRP* 5.4 4.0 - - + +
153B LEU* 4.5 12.1 - - + -
161B LEU* 4.3 14.4 - - + -
165B ILE* 4.1 19.1 - - + -
204B ILE* 4.6 2.7 - - + -
205B ILE* 3.6 18.4 - - + -
208B ILE* 3.5 28.7 - - + -
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.0 20.9 + - - +
91B ALA* 3.6 13.5 - - + +
92B ALA 3.3 0.2 - - - -
93B ILE* 1.3 78.5 - - - +
95B GLU* 1.3 57.1 + - - +
97B ILE* 3.4 2.8 + - - +
98B ARG* 3.0 17.5 + - - +
201B GLN* 3.0 45.5 + - + +
205B ILE* 3.8 32.3 - - + -
209B ARG* 5.3 7.7 - - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 3.2 10.4 + - - +
92B ALA* 3.7 8.7 - - - +
93B ILE 3.2 0.8 - - - -
94B LYS* 1.3 77.4 - - + +
96B TYR* 1.3 59.9 + - - +
98B ARG* 3.2 14.9 + - + +
99B LEU* 2.8 45.4 + - + +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP 4.1 12.9 + - - -
77B LEU* 5.0 1.4 - - - +
79B PRO* 3.8 26.9 - - + +
80B LEU* 3.7 34.0 - - + +
83B PHE* 4.0 23.1 - + + -
92B ALA 3.0 13.3 + - - +
93B ILE* 3.5 9.6 - - + +
95B GLU* 1.3 74.6 - - - +
97B ILE* 1.3 57.7 + - - +
99B LEU* 3.2 2.0 + - - -
100B LYS* 2.8 48.8 + - + +
162B ILE* 5.4 5.6 - - + -
165B ILE* 4.1 32.1 - - + -
166B TRP* 2.8 32.1 + + - -
212B URA 4.3 2.1 + - - -
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 36.4 + - + +
94B LYS* 3.6 5.4 - - - +
96B TYR* 1.3 72.0 - - - +
98B ARG* 1.3 61.9 + - - +
100B LYS* 3.2 2.5 + - - +
101B LEU* 2.8 41.2 + - + +
165B ILE* 4.1 22.2 - - + -
169B THR* 3.8 8.9 - - + +
197B VAL* 5.3 0.2 - - + -
200B VAL* 3.6 24.0 - - + -
201B GLN* 4.0 28.9 - - + -
204B ILE* 4.1 29.6 - - + -
205B ILE* 4.7 2.5 - - + -
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS 3.0 17.3 + - - +
95B GLU* 3.5 15.5 - - + +
97B ILE* 1.3 77.5 - - - +
99B LEU* 1.3 63.7 + - + +
101B LEU* 3.2 5.3 + - - +
102B GLU* 2.8 51.5 + - + +
193B PHE* 4.4 12.1 - - + -
194B ASN* 4.0 19.2 - - - +
197B VAL* 3.8 39.8 - - + +
198B GLU* 5.6 3.6 + - - -
201B GLN* 4.0 16.8 + - - +
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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
----------------------------------------------------------
79B PRO* 3.9 34.1 - - + -
95B GLU* 2.8 31.6 + - + +
96B TYR 3.8 2.9 - - - +
98B ARG* 1.3 77.2 - - + +
100B LYS* 1.3 57.3 + - - +
102B GLU* 3.2 28.8 + - - +
103B VAL* 3.0 35.0 + - + +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.2 43.1 + - + +
79B PRO* 5.8 0.9 - - + -
96B TYR* 2.8 44.0 + - + +
97B ILE* 3.6 4.0 - - - +
98B ARG 3.2 0.2 - - - -
99B LEU* 1.3 79.1 - - + +
101B LEU* 1.3 56.9 + - - +
103B VAL* 3.4 6.0 + - + +
104B SER* 3.0 28.6 + - - -
165B ILE* 4.6 4.0 - - + -
166B TRP* 4.1 9.6 - - - +
169B THR* 3.5 27.3 - - + +
170B GLN* 2.8 30.0 + - - +
212B URA 3.0 23.6 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 2.8 37.5 + - + +
98B ARG 3.8 2.9 - - - +
100B LYS* 1.3 68.8 - - - +
102B GLU* 1.3 67.6 + - - +
104B SER* 3.1 4.3 + - - -
105B ARG* 2.9 19.4 + - - +
169B THR* 3.8 21.5 - - + +
172B TYR* 3.9 32.3 - - + -
187B LEU* 3.7 6.5 - - + +
193B PHE* 3.6 21.3 - - + -
196B THR* 4.0 9.2 - - + +
197B VAL* 3.8 35.2 - - + +
200B VAL* 4.2 11.9 - - + -
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Residues in contact with GLU 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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98B ARG* 2.8 43.3 + - - +
99B LEU* 3.3 28.5 - - + +
101B LEU* 1.3 71.7 - - - +
103B VAL* 1.3 58.9 + - + +
105B ARG* 3.1 22.8 + - - +
106B ASP* 2.8 37.9 + - - +
193B PHE* 3.9 20.8 - - + -
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 6.1 0.7 - - + -
75B ILE* 4.0 28.7 - - + +
76B TRP* 3.4 35.9 - - + +
99B LEU* 3.0 18.8 + - + +
100B LYS* 3.7 6.5 - - + +
102B GLU* 1.3 75.7 - - + +
104B SER* 1.3 58.4 + - - +
106B ASP* 4.4 4.0 - - - +
107B TYR* 2.8 46.6 + - + +
110B ALA* 5.8 2.5 - - + -
111B SER* 6.3 0.9 - - - -
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Residues in contact with SER 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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76B TRP* 5.7 1.2 + - - +
100B LYS 3.0 15.0 + - - -
101B LEU* 3.1 8.7 + - - -
103B VAL* 1.3 79.3 - - - +
105B ARG* 1.3 60.5 + - - +
108B PRO* 3.4 24.0 - - - +
111B SER* 4.9 3.9 + - - -
169B THR 2.7 30.6 + - - -
170B GLN* 3.7 11.1 - - - +
173B ALA* 3.8 20.5 - - - +
187B LEU* 3.8 13.9 - - - +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU 2.9 13.3 + - - +
102B GLU* 3.4 26.5 + - - +
104B SER* 1.3 75.9 - - - +
106B ASP* 1.3 90.8 + - - +
108B PRO* 3.6 9.7 - - - +
187B LEU* 3.3 45.4 - - + +
188B ARG* 4.2 26.5 + - + +
193B PHE* 3.8 34.5 - - + +
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 2.8 26.5 + - - +
103B VAL* 4.3 3.4 - - - +
105B ARG* 1.3 104.9 + - - +
107B TYR* 1.3 62.7 + - + +
108B PRO* 3.2 10.3 - - - +
109B GLN* 4.2 2.8 + - - +
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 6.0 1.8 - - + -
75B ILE* 6.3 4.3 - - + -
103B VAL* 2.8 30.9 + - + +
106B ASP* 1.3 77.4 - - + +
108B PRO* 1.3 62.9 - - - +
109B GLN* 3.2 10.1 - - - +
110B ALA* 3.0 29.3 + - + +
111B SER* 3.4 4.3 + - - -
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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
------------------------------------------------------------
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