Contacts of the helix formed by residues 114 - 123 (chain B) in PDB entry 2AUW
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 SER 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ALA* 3.8 1.1 - - - -
113B ILE* 1.3 79.0 - - - +
115B ARG* 1.3 62.5 - - - +
116B ARG* 3.5 9.6 + - - +
117B MSE 3.0 32.0 + - - +
118B VAL* 3.1 23.0 + - - +
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Residues in contact with ARG 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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42A PRO* 3.9 18.1 - - + +
43A ASP* 2.6 43.8 + - - -
103B SER* 6.2 0.2 - - - -
104B LEU* 3.7 39.1 - - + +
105B THR* 3.0 31.2 + - - +
108B ALA* 3.7 13.3 - - + +
114B SER* 1.3 69.8 - - - +
116B ARG* 1.3 66.3 + - - +
118B VAL* 3.3 3.7 + - - +
119B SER* 3.0 22.7 + - - -
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Residues in contact with ARG 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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39A ARG* 3.1 24.0 + - - +
40A LYS* 2.8 45.3 + - - +
42A PRO* 3.8 19.3 - - + +
114B SER* 3.2 10.1 + - - +
115B ARG* 1.3 78.3 - - - +
117B MSE 1.3 60.6 - - + +
119B SER* 3.2 3.3 + - - -
120B TYR* 2.9 66.4 + - + -
1201B GOL 4.8 4.0 + - - +
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Residues in contact with MSE 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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113B ILE* 4.1 15.0 - - + -
114B SER* 3.0 28.3 + - - +
116B ARG* 1.3 76.1 - - + +
118B VAL* 1.3 66.5 + - - +
120B TYR* 3.2 4.7 + - - +
121B TYR* 3.0 56.8 + - + +
126B LYS* 3.8 41.5 - - + +
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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
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93B PHE* 3.5 14.2 - - + -
97B MSE 3.9 13.9 - - - -
104B LEU* 3.7 21.5 - - + +
107B ALA* 3.8 24.5 - - + -
108B ALA* 3.6 29.8 - - + +
111B LEU* 4.6 2.9 - - + -
113B ILE* 3.7 15.0 - - + +
114B SER 3.1 15.0 + - - +
115B ARG 3.5 7.6 - - - +
116B ARG 3.3 0.2 - - - -
117B MSE 1.3 77.6 - - - +
119B SER* 1.3 57.2 + - - +
121B TYR 3.4 0.2 + - - -
122B ARG* 2.9 30.3 + - - +
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Residues in contact with SER 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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42A PRO* 3.9 22.3 + - - -
45A ALA* 4.1 3.8 - - - +
104B LEU* 3.8 15.4 - - - +
115B ARG 3.0 13.4 + - - -
116B ARG 3.4 8.7 - - - -
118B VAL* 1.3 76.5 - - - +
120B TYR* 1.3 61.4 + - - +
122B ARG* 3.2 5.6 + - - +
123B THR* 2.8 34.5 + - - +
1201B GOL 2.8 30.7 + - - -
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Residues in contact with TYR 120 (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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39A ARG* 4.9 0.5 + - - +
116B ARG* 2.9 70.2 + - + +
117B MSE 3.2 8.9 + - - +
119B SER* 1.3 72.1 - - - +
121B TYR* 1.3 61.5 + - - +
123B THR* 3.8 3.8 - - - -
124B ALA 3.2 2.1 + - - -
125B HIS* 2.8 70.3 + + + -
126B LYS* 3.2 52.7 + - + -
1201B GOL 3.4 29.0 + - - -
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Residues in contact with TYR 121 (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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90B HIS* 3.3 18.9 - - - +
93B PHE* 3.9 16.8 - + + -
113B ILE* 3.7 27.2 - - + +
117B MSE 3.0 47.3 + - + +
118B VAL 3.7 3.4 - - - +
120B TYR* 1.3 73.2 - - - +
122B ARG* 1.3 65.4 + - - +
123B THR 3.4 0.3 + - - -
124B ALA* 3.4 4.5 + - - -
126B LYS* 3.7 23.1 - - + -
127B ILE 3.5 17.7 - - - -
128B ILE* 3.6 32.4 - - + +
129B PRO* 3.6 22.8 - - + +
132B ILE* 3.7 27.6 - - + +
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Residues in contact with ARG 122 (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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45A ALA* 5.8 0.4 - - - +
46A PRO* 4.4 9.3 - - - +
1B MSE 3.4 42.8 + - - +
2B ASN 2.8 28.3 + - - -
3B GLU* 3.2 43.4 + - - +
4B TYR 4.1 7.5 - - - +
90B HIS* 3.6 24.3 - - - +
93B PHE* 3.8 10.1 - - + -
94B GLY* 5.0 2.7 - - - -
97B MSE 3.2 40.3 - - + +
104B LEU* 4.3 7.9 - - - +
118B VAL 2.9 18.6 + - - +
119B SER* 3.2 5.8 + - - +
121B TYR* 1.3 77.7 - - - +
123B THR* 1.3 72.3 + - - +
124B ALA 3.4 0.4 - - - -
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Residues in contact with THR 123 (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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45A ALA* 4.7 2.9 - - + -
4B TYR* 3.4 41.1 - - + +
5B PHE* 3.7 3.9 - - - -
6B PHE* 2.9 25.8 + - - +
90B HIS* 5.4 0.2 - - - -
119B SER* 2.8 27.9 + - - +
120B TYR 3.4 5.2 + - - -
122B ARG* 1.3 96.1 - - - +
124B ALA* 1.3 63.1 + - - +
125B HIS* 3.3 2.3 + - - +
1201B GOL 2.7 26.5 + - - +
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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