Contacts of the strand formed by residues 130 - 143 (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 GLU 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A THR* 5.3 5.2 - - + +
72A VAL 3.3 8.1 - - - +
73A ARG* 3.9 30.1 + - + +
118A ALA* 3.4 6.6 - - - +
119A THR* 3.0 40.9 + - + +
121A ALA* 3.7 17.2 - - + +
122A VAL* 4.8 1.4 - - - +
128A GLN* 3.4 27.4 + - + +
129A PRO* 1.3 80.1 - - - +
131A TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.8 39.7 + + - -
48A MSE 4.6 2.2 - - + +
70A MSE 3.7 0.2 - - - +
71A THR* 3.3 8.7 - - - +
72A VAL* 2.8 43.2 + - + +
74A SER* 4.6 2.9 - - - -
77A PRO* 3.2 14.7 - - - +
78A PHE* 2.9 56.8 + + - -
116A LEU* 4.0 18.4 - - + -
117A GLN 3.3 9.2 - - - +
118A ALA* 3.6 28.9 - - + -
119A THR* 4.5 1.8 - - - -
129A PRO* 3.9 22.1 - - + +
130A GLU* 1.3 76.0 - - - +
132A TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 3.6 30.6 - - + +
70A MSE 3.2 29.4 - - - -
71A THR* 3.4 20.2 - - + +
115A HIS 4.0 1.6 - - - +
116A LEU* 3.6 2.9 - - - -
117A GLN* 2.9 31.9 + - - +
119A THR* 4.3 15.2 - - + +
131A TYR* 1.3 77.0 - - - +
133A ALA* 1.3 76.4 + - - +
134A THR* 3.7 25.1 - - + +
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Residues in contact with ALA 133 (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 10.2 - - + +
69A LYS* 3.5 0.9 - - - -
70A MSE 2.9 33.2 + - + +
112A GLY 3.6 24.5 - - - +
115A HIS* 3.8 11.4 - - + +
116A LEU* 3.8 19.7 - - + +
132A TYR* 1.3 84.0 - - - +
134A THR* 1.3 62.9 - - - +
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Residues in contact with THR 134 (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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67A MSE 5.3 2.4 - - - +
68A LEU* 3.1 15.8 + - - -
69A LYS* 3.7 13.2 - - - +
115A HIS* 5.7 3.3 - - - +
132A TYR* 3.7 25.3 + - + +
133A ALA* 1.3 76.7 - - - +
135A LEU* 1.3 69.1 + - - +
136A THR* 5.4 2.1 - - - +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.9 20.4 - - + -
67A MSE 3.4 2.1 - - - -
68A LEU* 2.9 49.6 + - + +
111A ILE* 3.8 28.3 - - + +
112A GLY* 5.2 0.4 - - - -
115A HIS* 3.9 31.0 - - + +
134A THR* 1.3 80.7 + - - +
136A THR* 1.3 75.9 + - - +
192A TYR* 4.2 13.9 - - + +
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Residues in contact with THR 136 (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* 3.3 13.7 - - - -
67A MSE 3.6 31.0 - - + -
134A THR* 5.4 2.5 - - - +
135A LEU* 1.3 88.3 - - - +
137A GLY* 1.3 59.7 + - - +
192A TYR* 3.8 12.3 - - - -
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Residues in contact with GLY 137 (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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65A ARG* 3.3 4.5 - - - +
66A PHE* 2.9 47.5 + - - +
136A THR* 1.3 77.8 - - - +
138A ARG* 1.3 67.5 + - - +
192A TYR* 3.3 12.8 - - - -
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Residues in contact with ARG 138 (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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63A LYS* 4.2 0.4 - - - +
64A PHE 3.3 7.4 - - - +
65A ARG* 3.9 15.9 - - + +
137A GLY* 1.3 81.1 - - - +
139A CYS* 1.3 66.6 + - - +
180A ASP* 2.6 40.0 + - - +
182A SER* 2.9 22.0 + - - -
184A GLU* 2.8 35.3 + - - +
185A LYS 3.1 19.8 + - - -
186A VAL* 3.3 19.4 - - + +
187A PRO* 3.3 15.6 - - - +
192A TYR* 3.2 15.9 + - - +
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Residues in contact with CYS 139 (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 3.5 0.9 - - - +
63A LYS* 3.3 3.1 - - - +
64A PHE* 2.9 65.8 + - - +
66A PHE* 3.9 18.4 - - - -
138A ARG* 1.3 79.1 - - - +
140A PHE* 1.3 59.8 - - - +
186A VAL* 3.8 13.2 - - - +
187A PRO 3.1 14.8 - - - +
188A HIS 3.9 1.1 - - - -
189A VAL* 3.6 30.3 - - - +
192A TYR* 4.0 5.6 - - + -
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Residues in contact with PHE 140 (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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61A TYR* 3.9 45.1 - + + -
62A GLU 3.2 1.8 - - - -
63A LYS* 4.0 30.7 - - + -
64A PHE* 4.4 2.9 - - - -
139A CYS* 1.3 73.4 - - - +
141A LEU* 1.3 58.4 + - - +
142A PRO* 3.7 3.7 - - + +
186A VAL* 3.9 32.3 - - + -
187A PRO 2.9 8.1 + - - +
188A HIS* 3.6 26.1 - + + -
189A VAL* 2.9 25.8 + - - +
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Residues in contact with LEU 141 (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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61A TYR* 3.5 2.3 - - - -
62A GLU* 2.8 35.2 + - + +
64A PHE* 3.8 17.4 - - + -
103A PRO* 5.2 2.0 - - + +
104A PHE* 3.7 33.2 - - + -
107A ILE* 4.1 21.8 - - + -
140A PHE* 1.3 71.9 - - - +
142A PRO* 1.3 78.2 - - - +
143A HIS* 3.5 13.7 - - + -
145A LEU* 6.0 0.7 - - + -
189A VAL* 4.0 8.3 - - + -
190A TRP* 3.8 24.7 - - + -
222A LEU* 4.2 22.7 - - + -
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Residues in contact with PRO 142 (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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59A LEU* 4.3 0.9 - - + -
60A ARG 3.3 7.6 - - - +
61A TYR* 3.7 25.6 - - + -
140A PHE 3.7 10.3 - - - +
141A LEU* 1.3 90.1 - - + +
143A HIS* 1.3 60.9 + - - +
188A HIS* 3.9 12.8 - - + +
190A TRP* 3.9 11.4 - - - +
219A THR* 3.8 15.3 - - + -
220A TRP 3.5 22.9 - - - +
221A VAL* 3.5 14.5 - - + -
222A LEU 3.0 20.1 + - - -
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Residues in contact with HIS 143 (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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58A SER 3.8 0.5 - - - +
59A LEU* 3.6 4.4 - - - +
60A ARG* 2.8 45.1 + - + +
62A GLU* 2.9 32.1 + - + -
104A PHE* 5.2 1.1 - + - -
141A LEU* 3.5 31.6 - - + -
142A PRO* 1.3 75.5 - - - +
144A ARG* 1.3 63.6 + - - +
145A LEU* 3.0 35.1 + - + +
146A GLY 3.1 29.2 - - - -
148A ILE* 3.7 13.8 - - + +
221A VAL* 4.0 2.2 - - - -
222A LEU* 3.2 22.0 - - + +
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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
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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