Contacts of the helix formed by residues 96 - 104 (chain B) in PDB entry 5X11
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.0 34.4 + - + +
34A TRP* 4.6 1.6 - - - -
94A VAL* 6.1 1.3 - - + -
160A LYS* 5.2 0.2 - - - -
164A ARG* 5.9 0.2 - - - +
94B VAL 4.3 0.7 - - - +
95B LYS* 1.3 76.6 - - - +
97B GLU* 1.3 63.3 + - - +
98B PHE* 2.9 22.2 + - - +
99B MET* 3.2 14.3 + - + +
100B LEU* 3.1 18.2 + - - +
124B ARG* 4.4 6.4 + - - -
168B TYR* 2.7 34.5 + - - -
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Residues in contact with GLU 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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1A MET* 4.3 18.9 - - - +
3A VAL* 4.0 30.1 - - + +
34A TRP* 4.5 10.3 - - + -
83A TRP* 2.9 38.9 + - + -
86A ARG* 5.7 0.2 + - - -
88A GLN* 4.4 18.7 - - - +
95B LYS 4.3 0.2 - - - -
96B ASP* 1.3 70.7 + - - +
98B PHE* 1.3 64.7 + - - +
100B LEU* 3.4 9.2 + - + +
101B LYS* 3.1 25.7 + - - +
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Residues in contact with PHE 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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96B ASP* 2.9 10.1 + - - +
97B GLU* 1.3 79.7 - - - +
99B MET* 1.3 63.1 + - - +
101B LYS* 3.0 16.6 + - + +
102B ALA* 2.9 23.6 + - + +
116B LEU* 4.0 32.3 - - + -
117B PHE* 3.7 39.9 - + - -
120B GLN* 3.7 38.8 - - + +
124B ARG* 5.3 1.1 - - - +
168B TYR* 3.3 20.6 - + - +
171B TRP* 4.1 7.6 - + - -
172B LEU* 3.7 24.0 - - + -
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Residues in contact with MET 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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33A PHE* 3.7 31.9 - - + -
156A LEU 3.6 10.3 - - - +
157A VAL* 4.0 17.5 - - + +
160A LYS* 3.5 36.1 - - + -
96B ASP* 3.2 28.2 + - - +
98B PHE* 1.3 78.9 - - - +
100B LEU* 1.3 66.3 + - - +
102B ALA* 3.0 23.3 + - + +
103B TYR* 3.0 14.0 + - - +
168B TYR* 3.9 8.3 - - - +
171B TRP* 3.5 34.3 - - + -
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Residues in contact with LEU 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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3A VAL* 3.5 32.8 - - + +
7A ALA* 4.0 24.7 - - + -
30A LEU* 3.8 27.1 - - + -
33A PHE* 4.9 2.1 - - - +
34A TRP* 4.0 19.3 - - + -
83A TRP* 3.9 15.5 - - + -
96B ASP 3.1 11.4 + - - +
97B GLU* 3.4 9.4 - - - +
98B PHE 3.2 0.2 - - - -
99B MET* 1.3 76.1 - - - +
101B LYS* 1.3 62.7 + - - +
103B TYR* 3.3 11.4 + - - +
104B PHE* 3.1 48.6 - - + -
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Residues in contact with LYS 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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83A TRP* 2.7 51.3 + - + +
84A LEU* 3.2 34.2 + - + +
86A ARG* 2.7 30.9 + - - +
88A GLN* 4.6 12.9 - - - +
97B GLU* 3.1 17.9 + - - +
98B PHE* 3.0 16.9 + - + +
100B LEU* 1.3 74.4 - - - +
102B ALA* 1.3 65.1 + - - +
104B PHE* 2.9 17.5 + - - +
105B ILE* 3.4 7.8 + - - -
108B LEU* 5.5 1.9 - - - +
116B LEU* 4.1 23.4 - - + +
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Residues in contact with ALA 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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153A GLY* 3.9 0.3 - - - -
156A LEU* 3.5 26.0 - - + +
98B PHE* 2.9 13.3 + - + +
99B MET* 3.0 35.6 + - + +
101B LYS* 1.3 75.7 - - - +
103B TYR* 1.3 62.2 + - - +
105B ILE* 3.0 27.6 + - - +
116B LEU* 6.2 0.2 - - - -
117B PHE* 4.3 18.8 - - + -
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Residues in contact with TYR 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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11A LEU* 4.0 13.7 - - + -
13A ARG* 3.6 23.3 + - - -
25A TYR* 3.7 20.8 + + - -
29A GLU* 2.7 38.7 + - + -
30A LEU* 3.7 43.4 - - + +
153A GLY* 3.8 22.4 - - - -
154A HIS* 4.2 9.4 - - + -
157A VAL* 3.7 25.9 - - + +
99B MET 3.0 9.7 + - - +
100B LEU 3.5 10.1 - - - +
101B LYS 3.2 0.2 - - - -
102B ALA* 1.3 77.4 - - - +
104B PHE* 1.3 70.6 + + - +
105B ILE* 3.2 3.0 + - - +
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Residues in contact with PHE 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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6A TYR 3.6 15.9 - - - -
7A ALA 3.3 20.6 - - - -
10A GLY* 3.3 33.9 - - - -
11A LEU* 3.4 11.0 - - + -
13A ARG* 3.6 21.9 + - - +
30A LEU* 4.9 0.2 - - + -
80A LEU* 4.7 1.3 - - + -
83A TRP* 4.0 15.9 - + - -
84A LEU* 4.2 15.7 - - + +
100B LEU* 3.1 46.9 + - + -
101B LYS* 2.9 9.3 + - - +
103B TYR* 1.3 94.4 - + - +
105B ILE* 1.3 64.2 + - - +
106B SER 3.2 2.9 - - - -
107B SER* 3.0 20.0 + - - -
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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