Contacts of the helix formed by residues 113 - 123 (chain I) in PDB entry 2QC8
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 LEU 113 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ILE* 6.1 0.6 - - - +
110I GLU 3.8 20.4 - - - +
111I THR* 3.3 11.8 + - - +
112I ASN* 1.3 74.3 - - - +
114I ARG* 1.3 63.3 + - - +
115I HIS 3.3 1.3 + - - -
116I THR* 3.9 5.1 + - - -
117I CYS* 3.3 20.1 + - - +
347I ASP* 3.8 28.7 + - + +
349I PHE* 3.8 16.8 - - + +
350I SER* 4.3 16.2 - - - +
353I GLU* 4.0 4.9 - - - +
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Residues in contact with ARG 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ALA* 3.5 31.1 + - - +
98I LEU* 5.0 4.3 - - - -
99I CYS 5.7 0.9 - - - -
100I GLU* 3.0 34.7 + - + +
112I ASN* 3.2 8.4 + - - +
113I LEU* 1.3 76.7 - - - +
115I HIS* 1.3 61.0 + - - +
117I CYS* 3.5 1.1 - - - +
118I LYS* 2.8 49.6 + - - +
212I ILE* 3.8 22.7 - - + +
216I ASP* 2.8 39.5 + - - -
349I PHE* 3.5 43.8 - - + -
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Residues in contact with HIS 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I GLU* 3.3 25.2 + - - +
102I PHE* 3.8 20.9 - + - -
108I PRO* 3.9 25.8 - - + +
112I ASN* 3.1 16.6 + - - +
113I LEU 3.3 0.6 - - - -
114I ARG* 1.3 79.0 - - - +
116I THR* 1.3 64.5 + - - +
118I LYS* 3.5 5.8 + - - +
119I ARG* 3.5 50.5 + - - +
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Residues in contact with THR 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ASN 5.1 1.3 + - - -
113I LEU* 3.9 7.1 + - - -
115I HIS* 1.3 77.5 - - - +
117I CYS* 1.3 66.9 + - - +
119I ARG* 3.4 13.1 + - - +
120I ILE* 3.2 22.0 + - + +
353I GLU* 3.2 26.0 - - - +
357I ARG* 3.5 16.6 - - - +
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Residues in contact with CYS 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LEU 3.3 13.6 + - - +
114I ARG 3.2 8.6 + - - +
116I THR* 1.3 76.5 - - - +
118I LYS* 1.3 58.1 + - - +
120I ILE* 3.1 5.4 + - - +
121I MET* 2.9 47.2 + - - +
212I ILE* 3.7 16.6 - - + -
349I PHE* 3.3 31.6 - - + +
352I THR* 3.4 17.7 - - - -
353I GLU* 2.9 19.8 + - - +
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Residues in contact with LYS 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I GLU* 5.5 1.8 - - - +
114I ARG* 2.8 37.0 + - - +
115I HIS* 3.8 6.5 - - - +
116I THR 3.3 0.2 - - - -
117I CYS* 1.3 72.9 - - - +
119I ARG* 1.3 64.4 + - + +
121I MET* 3.3 4.7 + - + +
122I ASP* 3.0 48.5 + - - +
212I ILE* 3.5 34.0 - - + +
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Residues in contact with ARG 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I HIS* 3.5 40.1 + - + +
116I THR* 3.4 14.5 + - + +
117I CYS 3.2 0.4 - - - -
118I LYS* 1.3 77.8 - - + +
120I ILE* 1.3 63.4 + - + +
122I ASP* 2.8 21.3 + - - +
123I MET* 2.9 31.7 + - + +
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Residues in contact with ILE 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I THR* 3.2 15.0 + - + +
117I CYS 3.1 8.6 + - - +
119I ARG* 1.3 76.3 - - + +
121I MET* 1.3 62.2 + - + +
123I MET* 3.2 34.1 + - + +
124I VAL* 3.5 10.4 - - - +
353I GLU* 4.0 20.4 - - + +
356I ILE* 3.4 34.4 - - + +
357I ARG* 3.7 35.9 - - + +
361I LEU* 3.7 24.0 - - + -
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Residues in contact with MET 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I CYS* 2.9 40.5 + - - +
118I LYS* 3.6 8.5 - - - +
119I ARG 3.1 0.4 - - - -
120I ILE* 1.3 77.8 - - + +
122I ASP* 1.3 62.0 + - - +
124I VAL* 3.4 7.1 + - - +
125I SER* 3.3 23.4 + - - -
129I PRO* 4.5 5.4 - - - +
131I PHE* 4.1 7.0 - - + -
211I GLY* 3.7 23.8 - - - -
212I ILE* 3.6 28.0 - - + +
352I THR* 3.6 25.8 - - - +
353I GLU* 4.0 2.7 - - - +
356I ILE* 3.5 33.9 - - + -
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Residues in contact with ASP 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I LYS* 3.0 46.3 + - - +
119I ARG* 2.8 11.8 + - - +
121I MET* 1.3 76.5 - - - +
123I MET* 1.3 59.9 + - + +
124I VAL 3.1 3.8 + - - -
125I SER* 3.8 17.9 + - - -
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Residues in contact with MET 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I ARG* 2.9 31.2 + - + +
120I ILE* 3.2 37.2 + - + +
122I ASP* 1.3 76.8 - - + +
124I VAL* 1.3 65.8 + - + +
125I SER 3.8 0.2 - - - -
127I GLN* 5.5 0.2 + - - -
361I LEU* 4.4 19.0 - - + +
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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