Contacts of the helix formed by residues 101 - 114 (chain A) in PDB entry 2W2R
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 LYS 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A MSE 3.2 27.0 + - + +
99A VAL 3.2 0.6 - - - -
100A GLY* 1.3 79.5 - - - +
102A ARG* 1.3 67.4 + - - +
103A PRO* 3.2 2.9 - - - -
104A PHE* 2.9 10.5 + - - +
105A TYR* 2.9 59.7 + - + +
151A MSE 3.8 28.3 - - + +
152A PHE* 2.8 30.8 + - - +
154A VAL* 3.6 19.2 + - - +
156A GLU* 4.2 1.1 + - - +
177A VAL* 3.1 23.1 + - + +
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 4.8 1.6 - - + -
92A ASP* 2.8 50.1 + - - +
93A ASN 4.8 2.4 + - - -
95A TYR* 3.6 55.3 + - + +
98A MSE 3.4 3.2 + - - -
99A VAL* 3.4 11.6 + - - +
101A LYS* 1.3 78.0 - - - +
103A PRO* 1.3 68.7 - - + +
105A TYR* 3.3 4.3 + - - +
106A LYS* 3.0 37.8 + - + +
229A LYS* 4.4 9.2 + - - -
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Residues in contact with PRO 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 3.9 6.1 - - - +
100A GLY* 3.7 11.7 - - - +
101A LYS 3.4 3.8 - - - -
102A ARG* 1.3 95.0 - - + +
104A PHE* 1.3 69.4 + - + +
106A LYS* 3.5 13.5 + - + +
107A ILE* 3.1 29.5 + - - +
141A LEU* 5.5 1.6 - - + -
145A LEU* 4.1 22.4 - - + -
148A ILE* 5.8 2.9 - - + -
210A LEU* 4.3 1.0 - - - +
222A LEU* 4.4 8.5 - - + -
225A LEU* 3.9 24.9 - - + -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.9 24.0 - - + -
64A PHE* 3.9 39.7 - + + -
100A GLY 3.8 12.3 - - - -
101A LYS 2.9 6.7 + - - +
103A PRO* 1.3 82.4 - - + +
105A TYR* 1.3 63.0 + - - +
107A ILE* 3.3 6.4 + - - +
108A ILE* 2.9 34.7 + - - +
141A LEU* 3.7 23.3 - - + -
143A HIS* 5.2 1.6 - + - -
145A LEU* 6.3 0.7 - - + -
148A ILE* 3.9 23.6 - - + -
151A MSE 3.7 33.4 - - + -
177A VAL* 3.9 22.9 - - + -
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 3.4 27.4 - + + -
95A TYR* 3.4 23.6 - - - -
101A LYS* 2.9 38.6 + - + +
102A ARG* 3.7 3.4 - - - +
104A PHE* 1.3 75.0 - - - +
106A LYS* 1.3 59.5 + - - +
108A ILE* 3.4 5.6 + - + +
109A ALA* 2.9 32.2 + - - +
154A VAL 4.6 1.4 + - - -
156A GLU* 2.6 43.0 + - + +
158A PHE* 4.0 12.8 - + - -
175A PHE* 3.5 42.6 + + + -
177A VAL* 3.9 25.0 + - + -
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TRP* 4.2 10.8 - - + +
92A ASP* 2.8 34.2 + - - +
102A ARG* 3.0 37.4 + - - +
103A PRO* 3.6 5.6 - - + +
105A TYR* 1.3 76.6 - - - +
107A ILE* 1.3 64.5 + - - +
109A ALA* 3.4 5.7 + - - +
110A LEU* 3.0 22.3 + - - +
208A PHE* 2.8 36.8 + - + +
209A GLY* 5.1 0.2 - - - -
210A LEU* 3.8 24.4 - - + +
225A LEU* 4.2 21.3 - - + -
229A LYS* 3.2 25.0 + - - -
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 5.0 4.3 - - + -
103A PRO 3.1 16.2 + - - +
104A PHE* 3.5 9.2 - - - +
105A TYR 3.2 0.2 - - - -
106A LYS* 1.3 80.3 - - - +
108A ILE* 1.3 61.1 + - + +
110A LEU* 3.2 6.0 + - + +
111A ILE* 3.0 28.6 + - + +
141A LEU* 4.1 22.0 - - + -
189A VAL* 3.9 33.2 - - + -
190A TRP* 3.6 31.0 - - + -
210A LEU* 3.7 28.9 - - + -
212A LEU* 4.6 2.5 - - + -
222A LEU* 4.5 5.6 - - + -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.1 16.6 - - + -
66A PHE* 4.0 30.5 - - + -
67A MSE 4.0 12.1 - - - +
68A LEU* 3.4 20.7 - - + +
70A MSE 4.2 0.3 - - - +
104A PHE 2.9 20.8 + - - +
105A TYR* 3.6 7.9 - - + +
107A ILE* 1.3 78.0 - - + +
109A ALA* 1.3 58.8 + - - +
111A ILE* 4.2 6.5 - - + -
112A GLY* 2.8 28.4 + - - -
175A PHE* 3.6 35.0 - - + -
177A VAL* 3.8 22.7 - - + -
189A VAL* 5.2 2.9 - - + -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MSE 3.6 9.6 - - + +
88A VAL* 3.9 6.5 - - + +
91A TRP* 3.9 15.3 - - + +
105A TYR 2.9 19.9 + - - +
106A LYS 3.6 4.9 - - - +
107A ILE 3.2 0.2 - - - -
108A ILE* 1.3 76.1 - - - +
110A LEU* 1.3 57.9 + - - +
113A SER* 3.0 31.2 + - - -
175A PHE* 3.8 21.1 - - + -
208A PHE* 3.8 17.3 - - + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.4 21.6 + - - +
85A THR* 4.8 0.2 - - + -
106A LYS 3.0 13.4 + - - +
107A ILE 3.2 8.5 + - - +
109A ALA* 1.3 77.2 - - - +
111A ILE* 1.3 65.8 + - + +
113A SER* 2.5 21.1 + - - +
190A TRP* 4.8 9.9 - - + -
193A MSE 4.1 13.7 - - + +
201A ILE* 4.4 15.7 - - + +
204A GLU* 4.0 19.5 - - + -
205A GLY* 4.1 12.6 - - - +
208A PHE* 3.7 31.8 - - + -
210A LEU* 4.1 19.1 - - + -
212A LEU* 4.5 8.7 - - + -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 5.3 3.6 - - + -
68A LEU* 5.2 1.1 - - + -
107A ILE* 3.0 21.7 + - + +
108A ILE* 3.8 7.9 - - + +
110A LEU* 1.3 81.6 - - + +
112A GLY* 1.3 62.9 + - - +
114A SER* 2.7 25.1 + - - -
115A HIS* 3.3 4.3 - - - -
135A LEU* 3.8 13.5 - - + -
189A VAL* 4.2 28.5 - - + +
190A TRP* 4.5 20.6 - - + -
192A TYR* 3.5 35.0 - - + +
193A MSE 3.8 29.8 - - + +
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.9 16.4 - - - +
70A MSE 3.8 17.7 - - - -
108A ILE 2.8 21.5 + - - -
111A ILE* 1.3 74.2 - - - +
113A SER* 1.3 62.8 + - - +
115A HIS* 2.9 21.3 + - - +
116A LEU 3.3 7.6 + - - -
133A ALA* 3.6 6.8 - - - +
135A LEU* 5.2 0.7 - - - -
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.7 10.9 - - - -
70A MSE 4.0 2.5 - - - +
81A TYR* 2.8 24.8 + - - -
84A VAL* 4.1 3.7 - - - +
85A THR* 3.7 8.3 - - - +
88A VAL* 4.1 25.1 - - - -
109A ALA 3.0 16.6 + - - -
110A LEU* 2.5 22.7 + - - -
112A GLY* 1.3 75.2 - - - +
114A SER* 1.3 59.3 + - - +
115A HIS 3.0 1.1 + - - -
116A LEU* 3.2 30.3 + - - +
208A PHE* 4.5 0.6 - - - -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.8 2.5 - - - -
81A TYR* 3.6 24.9 - - - -
111A ILE 2.7 20.6 + - - -
112A GLY 3.1 0.2 - - - -
113A SER* 1.3 79.8 + - - +
115A HIS* 1.3 59.1 + - - +
116A LEU 3.5 0.6 - - - +
117A GLN* 5.7 0.9 + - - -
193A MSE 3.8 15.4 - - - -
194A ASN* 2.9 55.3 + - - +
197A TYR* 3.7 13.7 - - - -
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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