Contacts of the helix formed by residues 109 - 120 (chain B) in PDB entry 1U8R
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 5.7 0.2 - - - +
100A GLU* 2.7 32.3 + - - -
103A ARG* 3.9 8.1 - - - +
78B LYS* 4.2 0.7 - - - -
107B VAL 3.3 2.3 + - - -
108B MET* 1.3 78.0 - - - +
110B GLU* 1.3 64.3 + - - +
111B ASP* 3.7 9.3 + - - +
112B VAL* 3.0 24.4 + - - +
113B GLU* 3.3 19.6 + - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 5.9 0.3 - - - +
77B ARG* 3.6 19.1 + - - +
78B LYS* 4.2 5.6 + - - +
108B MET 3.9 0.6 + - - -
109B SER* 1.3 71.3 - - - +
111B ASP* 1.3 66.4 + - - +
113B GLU* 3.2 33.8 - - - +
114B ARG* 3.2 41.8 + - - +
137B GLU 5.4 3.2 - - - +
138B LEU* 4.2 7.9 - - + -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.5 14.4 - - + -
96A GLU* 3.5 18.2 - - - +
109B SER* 3.1 9.3 - - - +
110B GLU* 1.3 74.8 - - - +
112B VAL* 1.3 66.7 + - - +
113B GLU 2.9 2.9 + - - -
114B ARG* 3.0 39.4 + - - +
115B ARG* 3.1 15.5 + - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.3 2.7 - - + -
90A ILE* 4.3 10.5 - - + -
92A LEU* 3.7 24.4 - - + +
100A GLU* 3.4 25.1 - - + +
104A TRP* 3.8 23.1 - - + -
108B MET* 3.9 13.9 - - + -
109B SER* 3.0 27.8 + - - +
111B ASP* 1.3 78.3 - - - +
113B GLU* 1.3 66.1 + - - +
115B ARG* 3.6 7.9 + - - +
116B LEU* 2.9 27.9 + - + +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 2.6 55.1 + - - +
78B LYS* 2.7 38.4 + - + +
81B LEU* 3.6 11.1 - - + +
108B MET* 3.9 19.7 - - + -
109B SER 3.3 13.3 + - - +
110B GLU* 3.2 12.9 - - - +
111B ASP 2.9 0.4 - - - -
112B VAL* 1.3 76.7 - - - +
114B ARG* 1.3 57.4 + - - +
116B LEU* 2.6 29.5 + - - +
117B VAL* 3.0 13.6 + - - +
138B LEU* 4.1 8.3 - - + -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 3.2 33.7 + - - +
111B ASP* 3.0 32.6 + - - +
113B GLU* 1.3 77.6 - - - +
115B ARG* 1.3 59.8 + - + +
117B VAL* 2.8 34.3 + - - +
118B LYS* 3.2 9.3 + - - +
138B LEU* 2.9 59.9 + - + +
139B GLY* 5.5 6.5 - - - +
140B VAL* 5.9 2.2 - - + -
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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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89A VAL 5.2 0.4 + - - -
90A ILE* 2.7 36.0 + - + +
91A GLY* 2.9 33.8 + - - -
92A LEU* 3.8 13.7 - - + +
93A PRO* 4.6 6.1 - - + -
111B ASP* 3.1 13.7 + - + +
112B VAL* 4.0 5.6 - - - +
114B ARG* 1.3 79.0 - - + +
116B LEU* 1.3 61.2 + - - +
118B LYS* 3.4 18.3 + - - +
119B VAL* 3.0 42.2 + - - +
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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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90A ILE* 3.8 12.6 - - + -
104A TRP* 5.8 0.4 - - + -
81B LEU* 4.6 19.5 - - + +
85B LEU* 3.4 50.3 - - + -
108B MET* 3.3 37.2 - - + -
112B VAL* 2.9 21.9 + - + +
113B GLU* 2.6 17.6 + - - +
115B ARG* 1.3 70.3 - - - +
117B VAL* 1.3 62.7 + - - +
119B VAL* 3.3 5.8 + - + +
120B LEU* 3.0 41.9 + - + +
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Residues in contact with VAL 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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81B LEU* 4.4 13.5 - - + -
113B GLU 3.0 10.3 + - - +
114B ARG* 2.8 15.4 + - - +
116B LEU* 1.3 79.2 - - - +
118B LYS* 1.3 63.9 + - - +
120B LEU 3.4 0.2 + - - -
121B ASN 3.2 5.2 + - - -
122B ASN* 2.8 53.9 + - - +
123B PRO* 3.6 10.1 - - + +
135B LEU* 4.0 25.4 - - + -
138B LEU* 4.3 12.6 - - + -
140B VAL* 4.3 22.9 - - + -
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Residues in contact with LYS 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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114B ARG 3.2 9.5 + - - +
115B ARG* 3.8 24.0 - - - +
116B LEU 3.3 0.2 - - - -
117B VAL* 1.3 80.3 - - - +
119B VAL* 1.3 61.5 + - + +
120B LEU 3.5 0.5 + - - -
121B ASN* 3.5 17.0 + - - +
122B ASN* 4.0 24.2 - - - +
140B VAL* 4.4 18.5 - - - +
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Residues in contact with VAL 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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89A VAL* 4.1 25.4 - - + +
90A ILE* 3.5 25.1 - - - +
85B LEU* 5.6 0.7 - - + -
89B VAL* 4.8 7.7 - - + +
115B ARG* 3.0 29.7 + - - +
116B LEU* 3.3 12.3 + - + +
118B LYS* 1.3 77.4 - - - +
120B LEU* 1.3 70.6 + - + +
121B ASN* 3.4 4.1 + - - -
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Residues in contact with LEU 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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81B LEU* 4.0 8.7 - - + +
84B ARG* 3.3 37.8 - - + -
85B LEU* 3.8 15.0 - - + +
88B ASP* 4.4 15.0 - - + +
89B VAL* 3.9 26.0 - - + -
116B LEU* 3.0 26.4 + - + +
119B VAL* 1.3 86.4 - - + +
121B ASN* 1.3 71.9 + - - +
122B ASN 3.7 0.2 - - - -
123B PRO* 3.6 24.8 - - + +
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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