Contacts of the helix formed by residues 115 - 133 (chain G) in PDB entry 2VKZ
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 THR 115 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G ASP* 4.4 8.1 - - - +
55G THR* 4.7 1.0 + - - -
109G LEU* 3.3 7.7 - - - +
113G ASP* 3.2 7.3 + - - +
114G THR* 1.3 82.3 + - - +
116G LEU* 1.3 67.4 + - - +
117G VAL* 3.7 19.1 - - + -
118G LYS* 3.4 51.0 - - + +
119G THR* 2.8 24.3 + - - -
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G LEU* 3.3 30.4 - - + +
114G THR* 5.2 2.7 - - + +
115G THR* 1.3 72.6 - - - +
117G VAL* 1.3 62.5 + - + +
119G THR* 3.2 7.8 + - + +
120G LYS* 3.0 51.9 + - - +
533G LEU 3.7 20.9 - - - +
534G ASP* 3.4 30.5 - - + +
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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
----------------------------------------------------------
51G ASP* 4.4 18.8 - - - +
115G THR* 3.7 17.5 - - + -
116G LEU* 1.3 81.2 - - + +
118G LYS* 1.3 55.8 + - - +
120G LYS* 3.7 10.5 + - + +
121G GLU* 3.2 27.2 + - + +
124G LYS* 4.3 6.8 + - - +
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Residues in contact with LYS 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G PHE 4.7 1.8 - - - -
49G ALA* 5.3 1.6 - - - +
50G ALA 2.9 24.6 + - - -
51G ASP* 3.0 25.8 + - - +
52G ASP 4.1 0.6 + - - -
53G GLU 2.7 27.4 + - - +
54G PRO* 5.2 0.2 - - + -
55G THR* 3.7 14.4 - - - +
59G GLU* 3.6 32.7 - - - +
113G ASP 5.0 1.1 - - - +
115G THR* 3.0 38.1 + - + +
117G VAL* 1.3 76.9 - - - +
119G THR* 1.3 60.9 + - - +
121G GLU* 3.1 15.7 + - + +
122G LEU* 3.0 27.7 + - - +
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Residues in contact with THR 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ALA* 3.4 19.8 + - + +
108G LEU* 5.2 3.5 - - - +
109G LEU* 3.4 30.8 - - + +
115G THR 2.8 7.1 + - - -
116G LEU* 3.2 14.6 - - + +
118G LYS* 1.3 73.3 - - - +
120G LYS* 1.3 69.0 + - + +
122G LEU* 3.0 9.8 + - - +
123G ILE* 3.0 22.1 + - + +
533G LEU* 3.3 40.2 - - + +
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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
----------------------------------------------------------
116G LEU* 3.0 38.5 + - - +
117G VAL* 3.8 9.4 - - + +
119G THR* 1.3 82.1 - - + +
121G GLU* 1.3 63.6 + - - +
123G ILE* 3.2 10.6 + - + +
124G LYS* 2.9 42.5 + - - +
175G ASP* 3.6 25.3 + - - +
179G THR* 4.4 13.6 - - + +
532G THR* 5.9 4.7 - - - +
533G LEU* 5.0 18.7 + - + +
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Residues in contact with GLU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ASP 4.2 14.9 - - - +
52G ASP* 4.4 2.3 - - - +
63G LYS* 3.6 38.7 + - - +
117G VAL* 3.2 17.4 + - + +
118G LYS* 3.1 19.3 + - - +
119G THR 3.2 0.4 - - - -
120G LYS* 1.3 73.6 - - - +
122G LEU* 1.3 63.8 + - - +
124G LYS* 3.0 26.2 + - + +
125G ASN* 2.9 37.8 + - - +
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ALA 3.9 3.8 - - - +
59G GLU* 3.6 36.3 - - + +
62G GLY* 3.8 23.9 - - - -
91G PHE* 3.9 22.7 - - + -
101G ILE* 4.1 12.6 - - + +
104G LEU* 4.0 20.6 - - + -
105G ALA* 5.6 4.0 - - + +
108G LEU* 4.5 12.3 - - + -
118G LYS 3.0 8.5 + - - +
119G THR* 3.0 11.9 + - - +
121G GLU* 1.3 78.3 - - - +
123G ILE* 1.3 63.5 + - + +
125G ASN* 3.4 6.6 + - - +
126G TYR* 3.1 20.8 + - - +
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Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ILE* 4.2 21.5 - - + -
102G HIS* 3.5 20.9 - - + +
105G ALA* 4.1 11.2 - - + -
119G THR* 3.0 15.0 + - + +
120G LYS* 3.6 11.2 - - + +
122G LEU* 1.3 74.2 - - + +
124G LYS* 1.3 67.3 + - - +
125G ASN 3.3 0.2 + - - -
126G TYR* 3.3 1.2 + - - +
127G ILE* 3.3 28.5 + - + +
179G THR* 4.2 5.2 - - + -
180G TYR* 3.8 32.5 - - + +
533G LEU* 2.9 38.1 - - + -
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Residues in contact with LYS 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G VAL* 4.3 7.1 + - - +
120G LYS* 2.9 43.7 + - - +
121G GLU* 3.3 31.6 - - + +
123G ILE* 1.3 72.1 - - - +
125G ASN* 1.3 63.8 + - - +
127G ILE* 4.3 1.2 - - - +
128G THR* 2.5 36.8 + - - +
178G GLN* 3.5 33.2 + - - +
179G THR* 3.7 44.6 - - + +
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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
----------------------------------------------------------
59G GLU 5.2 0.2 + - - -
62G GLY* 3.3 38.9 + - - +
63G LYS* 3.9 9.3 - - - +
65G LEU* 5.2 1.1 - - + -
66G GLY* 3.7 18.3 - - - -
121G GLU* 2.9 34.3 + - - +
122G LEU* 3.5 11.4 - - - +
123G ILE 3.1 0.2 - - - -
124G LYS* 1.3 80.8 - - - +
126G TYR* 1.3 57.7 + - - +
128G THR* 3.8 2.8 - - - -
129G ALA* 2.8 35.0 + - - +
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Residues in contact with TYR 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G GLY* 5.9 0.6 - - - -
65G LEU* 4.9 5.4 - - + -
88G LEU* 4.2 12.1 - - + +
91G PHE* 3.5 29.6 - + + -
92G GLU* 2.8 38.1 + - + +
96G LEU* 3.6 24.8 - - + +
100G ASP* 5.8 0.2 - - - -
101G ILE* 3.6 43.7 - - + -
122G LEU 3.1 7.8 + - - +
123G ILE 3.3 0.8 + - - +
125G ASN* 1.3 75.8 - - - +
127G ILE* 1.3 70.0 + - + +
129G ALA* 3.5 4.5 - - - +
130G ARG* 2.9 60.2 + - - +
137G PHE* 4.3 6.3 - + - -
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Residues in contact with ILE 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ILE* 3.2 30.3 - - + -
123G ILE* 3.3 11.3 + - + +
124G LYS* 4.3 1.3 - - - +
126G TYR* 1.3 78.9 - - - +
128G THR* 1.3 66.8 + - - +
130G ARG* 3.2 1.1 + - - +
131G ILE* 3.0 49.0 + - + +
137G PHE* 3.8 16.8 - - + -
179G THR 5.8 1.1 - - - +
180G TYR* 3.4 40.8 - - + -
182G VAL* 4.6 4.5 - - + -
183G LEU* 3.9 11.2 - - + -
255G LEU* 3.8 18.8 - - + -
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Residues in contact with THR 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G GLY* 6.5 0.7 - - - -
69G SER* 5.0 8.1 - - - -
124G LYS* 2.5 28.6 + - - +
125G ASN* 3.8 3.6 - - - -
127G ILE* 1.3 79.1 - - - +
129G ALA* 1.3 65.3 + - - +
131G ILE* 3.4 2.1 + - - +
132G MET* 3.2 35.4 + - - +
179G THR 4.0 10.2 + - - -
181G HIS* 5.3 1.2 + - - +
182G VAL* 3.3 24.2 - - + +
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Residues in contact with ALA 129 (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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65G LEU* 3.6 27.4 - - + +
69G SER* 3.2 28.7 - - - +
84G LEU* 3.9 4.5 - - + +
88G LEU* 4.2 4.7 - - + -
125G ASN 2.8 22.4 + - - +
126G TYR* 3.5 5.4 - - - +
128G THR* 1.3 73.6 - - - +
130G ARG* 1.3 64.2 + - - +
132G MET* 3.0 5.9 + - - +
133G ALA* 3.0 24.3 + - - +
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Residues in contact with ARG 130 (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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88G LEU* 3.9 17.7 - - + +
92G GLU* 4.0 11.6 + - - -
126G TYR* 2.9 51.4 + - + +
127G ILE* 3.6 5.2 - - - +
129G ALA* 1.3 79.0 - - - +
131G ILE* 1.3 62.7 + - + +
133G ALA* 3.2 9.2 + - - +
135G ARG* 3.1 55.3 + - + +
136G PRO 3.5 12.3 + - - -
137G PHE* 3.3 44.6 - - + +
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Residues in contact with ILE 131 (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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74G PRO* 4.9 6.1 - - - +
127G ILE* 3.0 22.9 + - + +
128G THR 4.0 0.2 - - - +
130G ARG* 1.3 77.4 - - - +
132G MET* 1.3 59.0 + - - +
133G ALA 3.2 0.4 + - - -
134G LYS* 3.5 12.6 + - - -
135G ARG 4.3 5.6 + - - +
136G PRO* 5.3 8.9 - - + +
137G PHE* 4.2 15.0 - - + -
182G VAL* 2.8 59.2 - - + +
183G LEU* 3.3 30.1 - - + -
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Residues in contact with MET 132 (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 SER* 3.0 30.3 - - - +
70G SER* 4.8 6.3 - - - +
72G VAL* 2.9 49.7 - - + +
73G GLU* 4.6 0.4 - - - +
74G PRO* 3.8 35.2 - - + +
84G LEU* 4.6 3.1 - - + -
128G THR* 3.2 28.9 + - - +
129G ALA* 3.0 5.8 + - - +
131G ILE* 1.3 74.4 - - - +
133G ALA* 1.3 55.7 + - - +
134G LYS* 3.1 8.3 + - - +
182G VAL* 5.6 6.1 - - + -
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Residues in contact with ALA 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G VAL* 5.7 0.7 - - - -
81G ASP* 6.4 2.5 - - - +
84G LEU* 3.5 25.1 - - + -
85G ASN* 3.5 26.0 + - - +
88G LEU* 3.7 19.5 - - + -
129G ALA 3.0 5.9 + - - +
130G ARG 3.2 10.0 + - - +
132G MET* 1.3 76.4 - - - +
134G LYS* 1.3 67.8 + - - +
135G ARG* 3.0 8.1 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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