Contacts of the helix formed by residues 106 - 120 (chain G) in PDB entry 2W3S
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 CYS 106 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ALA* 4.9 9.1 - - + -
105G PHE* 1.3 79.1 - - - +
107G THR* 1.3 70.7 + - - +
108G PRO* 3.5 1.1 - - - -
109G GLY* 3.3 12.7 + - - -
110G PHE* 3.4 34.4 + - + -
132G ASN* 5.5 0.7 + - + +
133G LEU 3.5 17.7 - - - +
134G CYS* 4.0 1.3 - - - -
142G ILE* 5.9 0.7 - - - -
1463G FES 2.3 48.2 - - - -
176H LEU* 4.0 10.3 - - + -
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Residues in contact with THR 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G MET* 4.2 10.6 - - + +
100G GLY 3.9 8.0 + - - -
101G SER* 3.2 26.6 - - - -
104G GLY* 2.6 29.9 + - - -
106G CYS* 1.3 75.9 - - - +
108G PRO* 1.4 69.4 - - - +
109G GLY 3.1 1.9 + - - -
110G PHE* 3.3 5.0 + - - +
111G ILE* 3.2 21.5 + - + +
15H HIS* 4.0 6.1 - - - +
16H VAL* 3.8 37.7 - - + -
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Residues in contact with PRO 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY 3.2 27.6 - - - +
35G THR* 5.0 3.6 - - - -
36G LYS* 4.2 11.9 - - + -
46G ALA 5.1 2.7 - - - +
48G THR 5.3 0.2 - - - -
78G ILE* 3.7 30.9 - - + +
104G GLY 3.4 6.7 - - - +
105G PHE* 3.4 16.2 - - - +
106G CYS 3.8 0.4 - - - -
107G THR* 1.4 88.6 - - + +
109G GLY* 1.3 55.6 + - - +
111G ILE* 3.3 3.3 + - - +
112G VAL* 3.0 33.2 + - - +
15H HIS 4.5 4.9 - - - +
18H GLY* 4.4 11.4 - - - -
22H TYR* 6.4 0.2 - - + -
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Residues in contact with GLY 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLY 3.7 19.1 - - - -
46G ALA* 4.4 9.9 + - - -
48G THR* 3.5 12.4 - - - -
106G CYS 3.3 8.0 + - - -
107G THR 3.1 0.8 - - - -
108G PRO* 1.3 78.2 - - - +
110G PHE* 1.3 63.3 + - - +
112G VAL 4.1 0.7 - - - -
113G SER* 3.2 17.2 + - - -
132G ASN* 2.9 20.5 + - - -
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Residues in contact with PHE 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G MET* 4.3 8.3 - - + -
106G CYS* 3.4 43.9 + - + -
107G THR* 3.3 7.7 + - - +
109G GLY* 1.3 75.9 - - - +
111G ILE* 1.3 52.9 + - - +
113G SER* 3.3 1.5 + - - -
114G MET* 2.6 54.5 + - + +
129G LEU* 4.1 14.6 - - + -
132G ASN* 3.3 43.5 - - + +
133G LEU 4.1 3.4 - - - -
134G CYS* 3.9 9.4 - - + -
139G TYR* 4.0 13.9 - + - -
142G ILE* 3.9 28.5 - - + -
701H PHE* 4.1 24.5 - + - -
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Residues in contact with ILE 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 3.1 24.5 - - + -
81G ILE* 3.8 21.5 - - + -
91G VAL* 3.6 8.1 - - + +
92G GLN* 3.6 21.8 - - + -
95G MET* 3.8 3.6 - - + -
107G THR* 3.2 16.2 + - + +
108G PRO 3.5 7.6 - - - +
110G PHE* 1.3 74.1 - - - +
112G VAL* 1.3 55.3 + - - +
114G MET* 3.5 20.9 - - + -
115G ALA* 2.7 37.2 + - - +
16H VAL* 3.4 39.7 - - + +
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Residues in contact with VAL 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G THR* 3.3 26.9 - - + +
49G VAL 3.3 33.7 - - - +
50G MET* 3.4 14.4 - - + +
59G ALA* 5.4 0.9 - - + -
77G THR* 4.2 4.5 - - - -
78G ILE* 3.5 32.8 - - + +
81G ILE* 4.4 6.7 - - + -
108G PRO 3.0 16.4 + - - +
109G GLY 4.3 0.2 - - - +
111G ILE* 1.3 75.5 - - - +
113G SER* 1.3 57.4 + - - +
115G ALA* 3.6 4.8 - - - +
116G ALA* 2.8 29.5 + - - +
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Residues in contact with SER 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G THR* 3.2 12.6 - - - +
59G ALA* 3.8 14.4 - - - +
109G GLY 3.2 14.5 + - - -
110G PHE 3.6 1.3 - - - -
112G VAL* 1.3 79.2 - - - +
114G MET* 1.3 62.8 + - - +
116G ALA* 3.3 3.1 + - - +
117G ALA* 3.0 22.3 + - - +
128G LEU* 4.7 3.0 + - - +
129G LEU* 3.5 26.4 - - - +
132G ASN* 3.4 1.4 + - - -
274G GLN* 3.0 29.3 + - - -
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Residues in contact with MET 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 3.7 19.6 - - + +
95G MET* 3.4 45.5 - - + +
110G PHE* 2.6 42.5 + - - +
111G ILE* 3.5 15.7 - - + +
113G SER* 1.3 72.1 - - - +
115G ALA* 1.3 57.3 + - - +
117G ALA* 3.2 7.4 + - - +
118G HIS* 2.9 28.1 + - - +
125G TYR* 6.2 3.4 - - + -
129G LEU* 4.2 20.4 - - + -
142G ILE* 4.0 21.8 - - - +
145G ALA* 5.3 0.9 - - - -
146G ALA* 5.0 14.4 - - + -
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Residues in contact with ALA 115 (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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50G MET* 4.8 2.2 - - - -
81G ILE* 3.8 34.5 - - + -
89G HIS* 4.0 12.4 + - + +
91G VAL* 3.8 9.3 - - + +
111G ILE 2.7 23.6 + - - +
112G VAL 3.6 3.6 - - - +
114G MET* 1.3 69.4 - - - +
116G ALA* 1.3 67.5 + - - +
118G HIS* 2.8 8.6 + - - +
119G ASP* 2.8 22.8 + - - +
158G LEU* 4.5 4.7 - - + +
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Residues in contact with ALA 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G MET* 3.8 25.2 - - + -
57G SER* 4.8 2.6 - - - +
58G ARG* 4.2 7.6 - - - +
59G ALA* 4.0 28.7 - - + +
112G VAL 2.8 19.9 + - - +
113G SER 3.6 4.9 - - - +
115G ALA* 1.3 72.4 - - - +
117G ALA* 1.3 61.4 + - - +
119G ASP* 3.1 14.4 + - - +
120G ARG* 3.3 15.8 + - - +
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Residues in contact with ALA 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 SER 3.0 17.0 + - - +
114G MET* 3.6 7.9 - - - +
115G ALA 3.0 0.4 - - - -
116G ALA* 1.3 73.2 - - - +
118G HIS* 1.3 63.5 + - - +
120G ARG* 3.6 2.3 - - - -
121G ASP* 3.2 2.1 + - - -
122G ARG* 2.7 41.6 + - - +
125G TYR* 5.0 7.0 - - + -
128G LEU* 3.8 35.4 - - + -
129G LEU* 6.4 0.4 - - + -
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Residues in contact with HIS 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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89G HIS* 3.5 21.9 + + + +
90G PRO* 3.9 17.0 - - + +
91G VAL* 4.6 7.0 - - + -
114G MET 2.9 13.6 + - - +
115G ALA 2.8 13.2 + - - +
117G ALA* 1.3 75.2 - - - +
119G ASP* 1.3 52.2 + - - +
120G ARG 3.0 0.9 - - - -
121G ASP* 2.8 26.1 + - - +
122G ARG 5.4 0.2 - - - -
146G ALA 6.0 0.2 - - - -
149G ALA* 3.1 25.0 + - + -
150G ALA* 4.2 7.5 + - - -
152G GLU* 3.0 28.1 + - - +
153G PRO 3.8 4.7 - - - -
154G PRO* 3.7 36.2 - - + +
155G ALA 4.2 0.8 + - - -
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Residues in contact with ASP 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G MET* 4.0 9.2 - - + -
52G ARG* 2.8 31.5 + - - -
57G SER* 2.6 26.5 + - - +
89G HIS* 5.7 0.6 + - - -
115G ALA 2.8 13.7 + - - +
116G ALA 3.1 11.0 + - - +
118G HIS* 1.3 72.1 + - - +
120G ARG* 1.3 59.1 + - - +
121G ASP 3.6 0.6 + - - -
154G PRO* 5.2 5.5 - - - +
155G ALA 4.5 3.1 + - - +
158G LEU* 4.1 10.2 - - + +
159G GLN* 3.3 42.0 + - - +
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Residues in contact with ARG 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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55G ALA 5.8 1.3 - - - -
56G GLY* 5.3 3.4 - - - -
57G SER* 2.9 41.7 + - - +
58G ARG* 4.9 7.9 - - - +
116G ALA 3.3 10.4 + - - +
117G ALA* 5.1 0.9 - - - +
118G HIS 3.0 0.6 - - - -
119G ASP* 1.3 80.0 - - - +
121G ASP* 1.3 71.5 + - - +
122G ARG* 2.8 52.8 + - + +
128G LEU* 5.7 3.0 - - - +
273G GLU* 4.7 10.5 + - - -
277G GLN* 4.8 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
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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