Contacts of the helix formed by residues 113 - 126 (chain G) in PDB entry 2EG5
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G SER 5.4 1.8 - - - +
65G GLY 4.6 16.8 - - - +
66G PRO* 5.4 4.9 - - + -
69G LEU* 3.9 19.5 - - + -
109G SER* 3.4 16.8 - - - +
110G VAL* 3.0 13.0 + - - +
112G LYS* 1.3 78.5 - - + +
114G LEU* 1.3 63.3 + - - +
115G PRO 3.5 0.7 - - - -
116G SER* 3.3 14.1 + - - +
117G PHE* 3.1 22.3 + - - +
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Residues in contact with LEU 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE* 3.6 21.8 - - + -
138E PRO* 4.0 1.1 - - + -
69G LEU* 3.8 22.4 - - + -
110G VAL* 3.5 12.3 + - + +
111G PHE* 3.1 35.0 + - + +
113G LEU* 1.3 75.1 - - - +
115G PRO* 1.3 71.2 - - + +
117G PHE* 3.1 8.3 + - + +
118G TYR* 2.9 38.8 + - + +
134G ILE* 3.6 54.5 - - + +
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Residues in contact with PRO 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE* 3.7 31.2 - - + -
111G PHE 3.6 8.7 - - - +
112G LYS 3.3 16.6 - - - +
113G LEU 3.6 0.4 - - - -
114G LEU* 1.3 90.8 - - + +
116G SER* 1.3 60.3 + - - +
118G TYR* 3.5 9.9 + - + +
119G ARG* 3.2 46.0 + - - +
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Residues in contact with SER 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LYS 5.3 0.4 + - - -
113G LEU* 3.3 19.0 + - - +
114G LEU 3.4 0.2 - - - -
115G PRO* 1.3 76.3 - - - +
117G PHE* 1.3 61.2 + - - +
119G ARG* 3.1 19.4 + - - +
120G LYS* 2.8 53.9 + - - +
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Residues in contact with PHE 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G LEU* 3.5 42.0 - - + -
72G VAL* 3.9 20.2 - - + -
73G ARG* 4.0 21.1 - - + -
76G VAL* 5.3 0.7 - - + -
113G LEU 3.1 18.3 + - - +
114G LEU* 3.1 8.7 + - + +
116G SER* 1.3 78.5 + - - +
118G TYR* 1.3 63.8 + + - +
120G LYS* 3.3 13.2 + - + +
121G LEU* 3.0 59.6 + - + +
134G ILE* 3.6 32.3 - - + -
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Residues in contact with TYR 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E PHE* 3.9 29.6 - + - -
137E MET* 4.5 5.4 - - + +
114G LEU* 2.9 27.7 + - + +
115G PRO* 3.9 6.7 - - + +
117G PHE* 1.3 85.0 - + - +
119G ARG* 1.3 57.7 + - - +
121G LEU* 3.5 15.9 + - + +
122G GLU* 3.1 24.9 + - - +
127G ARG 4.7 0.5 - - - +
129G ILE* 3.9 33.8 - - + +
130G GLY 5.9 1.6 - - - -
132G CYS* 3.2 26.4 + - + -
133G LEU* 4.1 0.9 - - - -
134G ILE* 3.0 55.2 + - + +
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Residues in contact with ARG 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G PRO* 3.2 29.2 + - - +
116G SER* 3.1 34.7 + - - +
118G TYR* 1.3 76.2 - - - +
120G LYS* 1.3 74.5 + - - +
122G GLU* 3.2 8.3 + - - +
123G LYS* 2.9 25.0 + - - +
129G ILE* 4.7 14.6 - - + -
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Residues in contact with LYS 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ARG* 6.3 2.9 - - - -
116G SER* 2.8 51.3 + - - +
117G PHE* 3.4 16.2 - - + +
119G ARG* 1.3 83.2 - - - +
121G LEU* 1.3 55.5 + - + +
123G LYS* 3.1 5.5 + - - -
124G GLU* 2.6 64.5 + - - +
125G ASN* 5.2 0.4 - - - -
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Residues in contact with LEU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ARG* 4.9 10.3 - - + -
76G VAL* 4.5 20.0 - - + -
77G GLN* 6.3 0.2 - - + -
117G PHE* 3.0 53.3 + - + +
118G TYR* 3.5 15.9 - - + +
120G LYS* 1.3 77.1 - - + +
122G GLU* 1.3 58.1 + - - +
125G ASN* 3.0 48.2 + - + +
126G GLY 3.2 4.2 + - - -
127G ARG* 3.3 17.5 + - + +
132G CYS* 3.9 30.7 - - + -
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Residues in contact with GLU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G TYR 3.1 10.5 + - - +
119G ARG* 3.2 10.1 + - - +
121G LEU* 1.3 77.4 - - - +
123G LYS* 1.3 63.7 + - - +
126G GLY* 3.5 17.1 + - - -
127G ARG 3.2 18.1 + - - +
128G LYS* 3.8 10.0 - - - +
129G ILE* 3.3 40.8 + - + +
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Residues in contact with LYS 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G ARG 2.9 16.9 + - - +
120G LYS* 3.6 6.1 - - - +
122G GLU* 1.3 80.3 - - - +
124G GLU* 1.3 71.1 + - + +
125G ASN 3.6 0.2 + - - -
126G GLY 4.4 1.4 + - - -
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Residues in contact with GLU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ARG* 5.6 6.1 - - - -
120G LYS* 2.6 44.7 + - - +
123G LYS* 1.3 84.8 - - + +
125G ASN* 1.3 67.7 + - - +
126G GLY 3.8 0.4 - - - -
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Residues in contact with ASN 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ARG* 5.3 1.6 - - - +
76G VAL* 4.6 10.1 - - + +
77G GLN* 3.1 48.8 + - - +
80G ASP* 4.4 6.8 + - - +
92G ARG* 3.0 26.5 + - - -
120G LYS 5.2 0.3 - - - -
121G LEU* 3.0 33.4 + - + +
124G GLU* 1.3 91.3 - - - +
126G GLY* 1.3 58.2 + - - +
127G ARG* 3.2 8.1 - - + +
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Residues in contact with GLY 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ARG* 3.7 21.3 + - - -
121G LEU 3.2 2.2 + - - -
122G GLU* 3.5 14.6 + - - -
123G LYS 4.4 1.8 + - - -
124G GLU 3.8 0.6 - - - -
125G ASN* 1.3 77.3 - - - +
127G ARG* 1.3 60.1 + - - +
128G LYS 3.6 3.1 + - - -
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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