Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 5C5B
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 MET 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A MET* 3.4 52.5 - - - +
47A ILE* 4.7 3.1 - - + -
48A TYR* 4.3 5.8 - - + +
107A LEU* 2.8 42.7 + - + +
110A ALA* 1.3 78.7 - - - +
112A MET* 1.3 87.1 + - + +
113A PHE 3.3 1.1 - - - -
114A PRO* 3.2 9.8 - - - +
115A ILE* 3.7 5.0 + - - +
199A PRO* 3.5 34.2 - - - +
202A GLY 4.8 0.2 - - - -
203A TYR* 3.8 31.6 - - + +
61B LEU* 6.3 0.9 - - - -
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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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41A TYR* 3.6 34.1 - - + +
44A MET* 3.6 35.4 - - - +
45A HIS* 3.7 23.1 - - + +
48A TYR* 3.9 26.9 - - + -
107A LEU 3.0 3.9 + - - +
108A ALA* 3.6 11.4 - - - +
111A MET* 1.3 95.1 - - + +
113A PHE* 1.3 55.8 + - - +
115A ILE* 3.3 4.7 - - + +
116A THR* 2.6 41.1 + - - +
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Residues in contact with PHE 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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108A ALA 3.1 13.1 + - - +
109A ASP* 3.4 23.6 - - - +
112A MET* 1.3 77.5 - - - +
114A PRO* 1.4 72.0 - - + +
116A THR* 3.7 6.2 - - + -
117A GLN* 2.9 61.5 + - + +
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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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109A ASP 3.6 6.3 - - - +
110A ALA* 3.2 24.5 - - - +
111A MET* 3.2 13.7 - - - +
113A PHE* 1.4 101.5 - - + +
115A ILE* 1.3 57.3 + - - +
117A GLN* 3.4 4.4 + - + +
118A PHE* 2.9 26.4 + - - +
195A ALA* 6.1 1.1 - - - -
198A GLU* 3.7 30.3 - - + +
199A PRO* 4.4 15.0 - - + -
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Residues in contact with ILE 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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37A MET* 3.8 26.2 - - + +
40A LEU* 3.9 15.9 - - + -
41A TYR* 3.5 50.7 - - + +
44A MET* 3.8 24.7 - - + -
111A MET 3.7 11.3 + - - +
112A MET* 3.3 18.2 - - + +
114A PRO* 1.3 76.6 - - - +
116A THR* 1.3 65.4 - - - +
118A PHE* 3.2 6.7 + - + +
119A LYS* 3.0 29.2 + - + +
195A ALA 5.4 1.1 - - - -
199A PRO* 4.5 8.7 - - + +
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Residues in contact with THR 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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41A TYR* 3.5 27.1 - - + +
112A MET* 2.6 29.8 + - - +
113A PHE* 3.7 7.4 - - + -
115A ILE* 1.3 78.6 - - - +
117A GLN* 1.3 58.7 + - + +
119A LYS* 3.2 3.2 + - - -
120A GLU* 2.9 43.6 + - + +
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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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113A PHE* 2.9 53.2 + - + +
114A PRO* 3.8 5.4 - - + +
116A THR* 1.3 75.4 - - + +
118A PHE* 1.3 61.5 + - - +
120A GLU* 4.4 3.1 - - + +
121A ARG* 2.9 79.6 + - + +
122A ASP* 3.5 3.4 - - - +
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Residues in contact with PHE 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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33A ILE* 4.3 5.6 - - + -
37A MET* 3.5 42.0 - - + -
114A PRO 2.9 15.0 + - - +
115A ILE* 3.2 12.1 + - - +
117A GLN* 1.3 78.4 - - - +
119A LYS* 1.3 59.3 + - + +
122A ASP* 3.3 27.8 + - + +
123A LEU* 3.1 45.7 + - + +
188A LEU* 4.0 29.4 - - + -
191A LYS* 3.9 14.8 - - + -
192A LYS* 4.2 8.3 - - - -
195A ALA* 3.5 28.3 - - + -
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Residues in contact with LYS 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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34A SER* 2.7 32.8 + - - +
37A MET* 5.5 3.4 - - + +
38A ASN* 3.4 37.8 - - + +
41A TYR* 5.9 9.9 - - + -
115A ILE* 3.0 16.9 + - + +
116A THR* 4.0 4.5 - - - +
118A PHE* 1.3 78.6 - - + +
120A GLU* 1.3 73.2 + - + +
123A LEU* 3.5 32.0 - - + +
124A LYS* 3.4 28.1 - - - +
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Residues in contact with GLU 120 (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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116A THR* 2.9 32.6 + - + +
117A GLN* 4.7 2.2 - - - +
119A LYS* 1.3 92.9 - - + +
121A ARG* 1.3 59.7 + - - +
124A LYS* 3.8 30.7 - - - +
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Residues in contact with ARG 121 (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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117A GLN* 2.9 53.0 + - + +
120A GLU* 1.3 80.6 - - - +
122A ASP* 1.3 86.9 + - - +
123A LEU 3.7 0.4 - - - -
124A LYS* 4.0 0.7 - - - +
125A GLU* 3.0 35.7 + - + +
191A LYS* 4.5 9.4 - - - +
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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