Contacts of the helix formed by residues 111 - 119 (chain A) in PDB entry 1RJG
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 ARG 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 5.9 2.6 - - - +
41A TYR* 5.5 6.3 - - + -
81A ARG 4.5 0.2 + - - -
82A THR* 3.6 31.0 + - + +
85A ILE* 3.5 33.4 - - - +
86A ASP* 3.4 22.2 + - - +
89A ILE* 3.7 19.6 - - - +
103A ASN* 4.5 1.6 - - - +
109A ASP* 3.0 38.5 + - - +
110A LEU* 1.3 74.8 - - - +
112A MET* 1.3 64.5 + - - +
113A LEU 3.2 0.9 - - - -
114A PRO* 3.4 10.7 - - + +
115A LEU* 3.2 35.9 + - + +
124A TYR* 3.7 17.3 - - - +
199A ILE* 4.4 11.2 - - - +
201A GLU* 3.4 18.6 + - - -
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP 3.4 26.7 - - - +
110A LEU* 3.6 23.8 - - + -
111A ARG* 1.3 81.0 - - - +
113A LEU* 1.3 74.6 + - + +
115A LEU* 3.8 3.8 - - - -
116A LEU* 3.0 39.1 + - + +
124A TYR* 3.6 41.1 - - + -
126A ASP* 3.4 19.3 - - - +
136A LYS* 4.2 4.5 - - - -
140A LEU* 4.5 9.2 - - + -
150A LEU* 4.9 0.9 - - + -
169A TYR* 3.5 35.2 - - + +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.5 33.8 - - + -
110A LEU* 3.6 25.5 + - + +
112A MET* 1.3 89.5 - - + +
114A PRO* 1.3 69.3 - - + +
116A LEU* 3.7 6.4 + - - +
117A GLN* 3.3 21.7 + - - +
140A LEU* 5.2 0.4 - - + -
146A LEU* 3.7 29.2 - - + +
149A SER* 3.4 24.2 - - - +
150A LEU* 3.6 33.4 - - + -
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Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.0 26.0 - - + -
37A LEU* 4.3 8.6 - - + +
41A TYR* 4.2 20.9 - - + -
44A TRP* 3.4 18.1 - - + -
110A LEU 3.3 13.0 - - - +
111A ARG* 3.4 16.8 - - + +
113A LEU* 1.3 97.3 - - + +
115A LEU* 1.3 60.9 + - + +
117A GLN* 3.5 5.2 + - + +
118A MET* 3.2 31.7 + - - +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 4.9 6.5 - - - +
89A ILE* 4.2 20.2 - - + -
90A LEU* 4.9 7.6 - - + -
93A LEU* 3.6 27.4 - - + -
101A VAL* 5.9 1.3 - - + -
111A ARG* 3.2 45.4 + - + +
112A MET* 3.9 5.4 - - - +
113A LEU 3.3 0.8 - - - -
114A PRO* 1.3 79.8 - - + +
116A LEU* 1.3 61.1 + - - +
118A MET* 4.0 9.2 - - + -
119A PHE* 3.3 30.8 + - + +
122A LEU* 3.2 24.9 - - + +
124A TYR* 4.4 13.0 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A MET* 3.0 29.5 + - + +
113A LEU* 4.1 5.4 - - + +
114A PRO 3.3 0.4 - - - -
115A LEU* 1.3 75.4 - - - +
117A GLN* 1.3 64.5 + - + +
119A PHE 3.1 19.5 - - - +
120A PRO* 4.2 1.0 - - - +
122A LEU* 3.3 31.0 - - + +
124A TYR* 4.6 7.4 - - + -
149A SER 5.7 4.3 - - - +
150A LEU* 3.9 29.8 - - + -
168A ARG* 3.5 47.8 + - + +
169A TYR* 4.2 15.7 - - + -
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP* 5.0 1.0 + - - -
37A LEU* 3.4 33.3 - - + +
40A LYS* 3.6 20.2 + - - +
44A TRP* 4.3 10.6 - - + -
113A LEU 3.3 18.2 - - - +
114A PRO 3.5 4.7 + - - +
115A LEU 3.4 0.2 - - - -
116A LEU* 1.3 77.3 - - + +
118A MET* 1.3 63.9 + - - +
119A PHE 4.8 0.9 - - - -
120A PRO* 4.9 5.0 - - - +
149A SER* 4.3 21.9 - - - +
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Residues in contact with MET 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN 4.0 5.2 - - - +
32A ARG* 4.0 20.9 - - + +
33A LEU* 3.9 22.9 - - - -
37A LEU* 3.5 18.2 - - + -
90A LEU* 3.8 29.2 - - + -
114A PRO* 3.2 22.3 + - - +
115A LEU* 4.5 7.2 - - + -
116A LEU 3.4 0.2 - - - -
117A GLN* 1.3 78.6 - - - +
119A PHE* 1.3 79.6 + - + +
120A PRO* 3.5 9.2 - - - +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.0 16.8 - - + -
93A LEU* 3.3 65.3 - - + -
94A VAL* 4.3 12.3 - - + -
97A GLU* 5.4 7.2 - - + +
115A LEU* 3.3 24.1 + - + +
116A LEU 3.1 13.2 - - - +
118A MET* 1.3 106.4 - - + +
120A PRO* 1.3 68.3 - - + +
121A HIS 3.3 2.5 + - - +
122A LEU* 3.4 19.6 - - + +
168A ARG* 3.2 7.3 + - - -
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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