Contacts of the helix formed by residues 101 - 122 (chain G) in PDB entry 4YC6
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 ASP 101 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G TYR 3.4 5.6 + - - -
100G MET* 1.3 70.8 - - - +
102G SER* 1.3 56.4 + - - +
103G SER* 2.6 31.1 + - - -
104G LEU* 2.6 44.3 + - + +
105G VAL 3.1 4.3 + - - -
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Residues in contact with SER 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G MET 3.1 8.1 + - - -
101G ASP* 1.3 72.0 - - - +
103G SER* 1.3 60.5 + - - +
105G VAL* 3.5 13.2 - - - +
106G LYS* 3.3 26.8 + - - +
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Residues in contact with SER 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASP* 2.6 22.2 + - - -
102G SER* 1.3 81.4 + - - +
104G LEU* 1.3 58.7 + - - +
106G LYS* 3.7 11.6 - - - +
107G SER* 3.0 24.9 + - - -
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Residues in contact with LEU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G TYR* 3.8 22.2 - - - +
100G MET* 4.1 14.4 - - + -
101G ASP* 2.6 29.7 + - + +
103G SER* 1.3 75.5 + - - +
105G VAL* 1.3 53.4 + - - +
107G SER* 4.1 9.4 - - - +
108G TYR* 2.8 73.9 + - + +
140G GLY 5.8 0.4 - - - +
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G MET* 3.8 39.2 - - + +
101G ASP 3.1 9.7 + - - +
102G SER* 3.5 13.9 - - - +
104G LEU* 1.3 74.8 - - - +
106G LYS* 1.3 54.4 - - - +
108G TYR* 3.0 6.0 + - - +
109G LEU* 2.8 40.3 + - + +
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Residues in contact with LYS 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G SER 3.3 14.5 + - - +
103G SER* 3.7 11.0 - - - +
105G VAL* 1.3 78.9 - - - +
107G SER* 1.3 67.9 + - - +
109G LEU* 3.4 7.0 + - - +
110G TYR* 3.2 22.5 + - + +
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Residues in contact with SER 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G SER 3.0 16.5 + - - -
104G LEU* 3.4 16.9 + - - +
106G LYS* 1.3 78.1 - - - +
108G TYR* 1.3 66.7 + - - +
110G TYR* 3.2 5.6 + - - +
111G GLN* 2.6 47.8 + - - +
140G GLY 5.2 0.5 + - - -
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Residues in contact with TYR 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G LEU* 3.9 29.2 - - + -
90G TYR* 4.8 9.9 - + - -
100G MET* 4.2 18.6 - - + -
104G LEU* 2.8 55.5 + - + +
105G VAL* 3.5 4.9 - - - +
107G SER* 1.3 72.5 + - - +
109G LEU* 1.3 63.9 + - - +
111G GLN* 3.2 16.5 + - - +
112G ILE* 2.9 36.5 + - + +
136G ILE* 3.6 28.3 - - + +
140G GLY* 4.1 22.5 + - - -
142G ILE* 3.9 18.1 - - + +
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Residues in contact with LEU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G VAL* 2.8 24.6 + - + +
106G LYS* 3.9 6.7 - - - +
108G TYR* 1.3 74.4 - - - +
110G TYR* 1.3 52.1 + - - +
112G ILE* 3.2 18.8 + - + +
113G LEU* 2.7 55.2 + - + +
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Residues in contact with TYR 110 (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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106G LYS* 3.2 12.4 + - + +
107G SER* 3.5 10.8 - - - +
109G LEU* 1.3 77.3 - - - +
111G GLN* 1.3 61.9 + - + +
113G LEU* 3.3 13.2 + - + +
114G GLN* 2.8 70.8 + - + +
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Residues in contact with GLN 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ASN* 3.3 36.6 - - - +
107G SER* 2.6 35.6 + - - +
108G TYR* 3.5 8.3 - - - +
110G TYR* 1.3 82.0 - - + +
112G ILE* 1.3 61.1 + - - +
114G GLN* 3.3 7.6 + - - +
115G GLY 3.1 17.3 + - - -
140G GLY 3.8 6.2 + - - +
141G THR* 3.5 14.5 + - - +
142G ILE* 3.2 43.5 - - + +
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Residues in contact with ILE 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G LEU* 5.4 3.1 - - + -
108G TYR* 2.9 29.6 + - + +
109G LEU* 3.5 19.1 - - + +
111G GLN* 1.3 73.2 - - - +
113G LEU* 1.3 67.1 + - + +
115G GLY* 3.3 2.9 + - - -
116G ILE* 3.1 23.2 + - + +
129G LEU* 5.1 11.4 - - + -
134G LEU* 3.6 36.1 - - + -
142G ILE* 4.0 23.1 - - + -
144G LEU* 4.2 19.4 - - + +
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Residues in contact with LEU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G LEU* 2.7 46.9 + - + +
110G TYR* 3.5 12.8 - - + +
112G ILE* 1.3 72.9 - - + +
114G GLN* 1.3 58.3 + - + +
116G ILE* 3.2 17.9 + - + +
117G VAL* 2.9 39.6 + - + +
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Residues in contact with GLN 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G HIS* 3.8 14.9 + - + +
62G ASN* 3.7 17.2 + - - +
110G TYR* 2.8 56.7 + - + +
111G GLN* 3.3 9.8 + - - +
113G LEU* 1.3 74.9 - - + +
115G GLY* 1.3 58.1 + - - +
117G VAL* 3.8 5.7 - - - +
118G PHE* 3.0 29.5 + - - +
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Residues in contact with GLY 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G HIS* 4.2 4.0 - - - -
62G ASN* 3.7 27.7 - - - +
63G ILE* 3.8 9.5 - - - +
111G GLN 3.1 10.3 + - - -
112G ILE 3.3 2.9 + - - -
113G LEU 3.3 0.4 - - - -
114G GLN* 1.3 76.5 - - - +
116G ILE* 1.3 57.8 + - - +
118G PHE* 3.5 3.9 + - - +
119G CYS* 3.1 32.2 + - - -
144G LEU* 4.3 5.6 - - - -
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Residues in contact with ILE 116 (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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112G ILE* 3.1 16.4 + - + +
113G LEU* 3.2 29.6 + - + +
115G GLY* 1.3 76.3 - - - +
117G VAL* 1.3 63.6 + - + +
119G CYS* 3.0 11.1 + - + +
120G HIS* 2.8 74.1 + - + +
126G HIS* 4.5 20.4 - - + +
129G LEU* 4.9 11.2 - - + -
144G LEU* 3.8 21.7 - - + +
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Residues in contact with VAL 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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113G LEU* 2.9 26.7 + - + +
114G GLN* 3.8 6.1 - - - +
116G ILE* 1.3 82.7 - - + +
118G PHE* 1.3 51.0 + - - +
120G HIS* 3.2 10.1 + - - +
121G SER* 2.5 36.6 - - - -
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Residues in contact with PHE 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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58G LEU* 3.9 28.0 - - + -
59G ARG 3.2 31.9 - - - -
60G HIS* 3.4 38.6 - + + -
63G ILE* 4.2 10.8 - - + -
114G GLN 3.0 10.7 + - - +
115G GLY 3.5 9.2 - - - +
116G ILE 3.2 0.2 - - - -
117G VAL* 1.3 78.5 - - - +
119G CYS* 1.3 64.5 + - - +
121G SER* 2.9 23.3 + - - -
122G ARG* 3.2 50.2 + - - +
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Residues in contact with CYS 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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58G LEU* 5.1 4.7 - - - -
63G ILE* 4.1 16.8 - - - -
115G GLY 3.1 21.0 + - - +
116G ILE* 3.0 15.8 + - + +
118G PHE* 1.3 86.7 - - - +
120G HIS* 1.3 60.3 + - + +
122G ARG* 3.1 10.2 + - - +
124G VAL* 2.9 45.1 + - + +
125G LEU* 5.5 1.1 - - - -
144G LEU* 4.8 5.6 - - - -
147G PHE* 4.1 30.7 - - - -
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Residues in contact with HIS 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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116G ILE* 2.8 54.1 + - + +
117G VAL* 3.2 7.3 + - - +
118G PHE 3.1 3.4 - - - -
119G CYS* 1.3 73.6 - - - +
121G SER* 1.3 53.9 + - - +
122G ARG 3.2 0.7 - - - -
123G ARG* 2.7 28.9 + - - -
124G VAL 3.3 18.3 + - - -
125G LEU* 3.9 23.3 - - + +
126G HIS 5.1 0.4 + - - -
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Residues in contact with SER 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G VAL* 2.5 35.2 - - - -
118G PHE* 2.9 17.6 + - - -
120G HIS* 1.3 66.0 + - - +
122G ARG* 1.3 70.8 + - - +
123G ARG* 3.4 2.8 + - - +
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Residues in contact with ARG 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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58G LEU* 4.3 18.8 - - + +
118G PHE* 3.2 56.3 + - - +
119G CYS* 3.1 12.1 + - - +
121G SER* 1.3 98.7 + - - +
123G ARG* 1.3 69.4 + - - +
124G VAL* 3.2 17.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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