Contacts of the helix formed by residues 109 - 120 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G LEU* 5.5 0.2 - - - +
100G GLU* 2.7 32.1 + - - -
103G ARG* 3.8 10.8 - - - +
78H LYS* 4.0 0.4 - - - -
107H VAL 3.3 2.0 + - - -
108H MET* 1.3 77.1 - - - +
110H GLU* 1.3 64.3 + - - +
111H ASP* 3.2 9.6 + - - +
112H VAL* 3.1 21.0 + - - +
113H GLU* 3.2 19.2 + - - +
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ALA* 5.8 0.7 - - - +
77H ARG* 3.5 29.6 + - - +
78H LYS* 4.0 6.4 + - - +
108H MET 3.9 0.6 + - - -
109H SER* 1.3 73.9 - - - +
111H ASP* 1.3 64.2 + - - +
113H GLU* 3.3 13.3 - - - +
114H ARG* 3.3 52.7 + - - +
137H GLU 5.3 3.4 - - - +
138H LEU* 4.2 7.4 - - + -
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Residues in contact with ASP 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 4.4 16.6 - - + -
96G GLU* 3.5 18.3 - - - +
109H SER* 3.1 8.6 - - - +
110H GLU* 1.3 75.3 - - - +
112H VAL* 1.3 65.7 + - - +
113H GLU 3.0 2.1 + - - -
114H ARG* 3.1 30.2 + - - +
115H ARG* 3.1 24.1 + - - +
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G LEU* 4.2 3.4 - - + -
90G ILE* 4.3 12.7 - - + +
92G LEU* 3.6 26.0 - - + -
100G GLU* 3.3 25.6 - - + +
104G TRP* 3.8 22.4 - - + -
108H MET* 4.0 5.4 - - + -
109H SER* 3.1 22.5 + - - +
111H ASP* 1.3 75.5 - - - +
113H GLU* 1.3 62.1 + - - +
115H ARG* 3.5 6.7 + - - +
116H LEU* 2.9 40.1 + - + +
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Residues in contact with GLU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ARG* 2.6 54.6 + - - +
78H LYS* 2.5 41.3 + - + +
81H LEU* 3.8 9.9 - - + +
108H MET* 3.7 22.0 - - + -
109H SER 3.2 14.1 + - - +
110H GLU* 3.3 11.9 - - - +
111H ASP 3.0 0.2 - - - -
112H VAL* 1.3 76.5 - - - +
114H ARG* 1.3 66.4 + - - +
116H LEU* 2.7 18.1 + - - +
117H VAL* 3.0 15.6 + - - +
138H LEU* 4.1 7.9 - - + -
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Residues in contact with ARG 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H GLU* 3.3 35.0 + - - +
111H ASP* 3.1 33.1 + - - +
113H GLU* 1.3 78.7 - - - +
115H ARG* 1.3 64.8 + - + +
117H VAL* 3.0 28.2 + - - +
118H LYS* 3.3 9.6 + - - +
138H LEU* 2.8 68.2 + - + +
139H GLY* 5.4 7.0 - - - +
140H VAL* 5.8 2.7 - - + -
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Residues in contact with ARG 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G VAL 5.3 0.4 + - - -
90G ILE* 2.6 35.3 + - + +
91G GLY* 2.7 33.5 + - - -
92G LEU* 3.9 12.6 - - + +
93G PRO* 4.7 6.1 - - - -
111H ASP 3.1 14.7 + - - +
112H VAL* 3.9 4.7 - - - +
114H ARG* 1.3 80.2 - - + +
116H LEU* 1.3 62.6 + - - +
118H LYS* 3.4 18.4 + - - +
119H VAL* 3.1 42.8 + - - +
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G ILE* 3.9 12.6 - - + -
104G TRP* 5.7 0.7 - - + -
81H LEU* 4.8 14.4 - - + +
82H ALA 5.3 0.2 - - - +
85H LEU* 3.5 53.6 - - + -
108H MET* 3.4 35.0 - - + -
112H VAL* 2.9 22.8 + - + +
113H GLU* 2.7 13.6 + - - +
115H ARG* 1.3 71.8 - - - +
117H VAL* 1.3 66.2 + - - +
119H VAL* 3.2 6.0 + - + -
120H LEU* 2.9 43.4 + - + +
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Residues in contact with VAL 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H LEU* 4.2 17.3 - - + -
113H GLU 3.0 14.2 + - - +
114H ARG* 3.0 14.1 + - - +
116H LEU* 1.3 78.6 - - - +
118H LYS* 1.3 60.1 + - - +
120H LEU 3.5 0.2 + - - -
121H ASN 3.2 4.0 + - - -
122H ASN* 2.7 58.8 + - + +
123H PRO* 3.5 10.1 - - + +
135H LEU* 4.0 25.4 - - + -
138H LEU* 4.3 8.7 - - + -
140H VAL* 4.3 22.0 - - + -
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Residues in contact with LYS 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H ARG 3.3 10.1 + - - +
115H ARG* 3.8 22.4 - - - +
116H LEU 3.2 0.2 - - - -
117H VAL* 1.3 80.5 - - - +
119H VAL* 1.3 61.8 + - + +
121H ASN* 3.4 18.9 + - - +
122H ASN* 3.9 24.2 - - - +
140H VAL* 4.3 20.5 - - - +
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Residues in contact with VAL 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G VAL* 4.1 22.7 - - + +
90G ILE* 3.7 23.3 - - + +
85H LEU* 5.6 0.7 - - + -
89H VAL* 4.8 12.4 - - + +
115H ARG* 3.1 30.3 + - - +
116H LEU* 3.2 13.7 + - + +
118H LYS* 1.3 76.7 - - - +
120H LEU* 1.3 68.8 + - + +
121H ASN* 3.4 5.0 + - - -
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LEU* 3.9 12.6 - - + +
84H ARG* 3.1 35.3 - - + -
85H LEU* 4.0 14.4 - - + +
88H ASP* 4.3 15.7 - - + +
89H VAL* 3.9 25.8 - - + -
116H LEU* 2.9 30.4 + - + +
119H VAL* 1.3 84.2 - - + +
121H ASN* 1.3 72.6 + - - +
122H ASN 3.6 0.7 - - - -
123H PRO* 3.5 23.3 - - + +
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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
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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