Contacts of the strand formed by residues 134 - 148 (chain E) in PDB entry 2P6T
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 VAL 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E VAL* 3.9 17.5 - - + -
75E SER 4.4 0.4 - - - -
76E ILE* 3.8 4.7 - - + -
86E PHE* 3.5 35.4 - - + -
128E LEU* 2.9 35.4 - - + +
129E LEU* 3.9 25.7 - - + +
131E HIS* 3.2 17.8 + - + +
132E HIS 4.1 1.2 - - - +
133E GLY* 1.3 75.5 - - - +
135E GLN* 1.3 60.5 + - - +
136E ASP 4.0 5.2 - - - +
78G LYS* 3.7 18.0 - - - +
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E SER* 3.1 19.5 + - - +
76E ILE 4.3 1.3 - - - -
77E ARG* 3.2 41.7 - - + +
78E LYS* 4.4 8.0 + - - +
129E LEU* 5.8 0.7 - - - -
133E GLY 3.2 2.6 + - - -
134E VAL* 1.3 75.0 - - - +
136E ASP* 1.3 67.8 + - + +
78G LYS* 4.6 21.6 - - + +
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Residues in contact with ASP 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ARG 4.9 0.2 - - - -
74E VAL* 3.4 7.1 - - - +
75E SER* 2.8 38.9 + - - -
129E LEU* 4.8 4.1 - - - +
134E VAL* 3.6 5.1 - - - -
135E GLN* 1.3 84.1 - - + +
137E ALA* 1.3 76.8 + - - +
138E GLN* 6.3 0.2 - - - -
162E CA 3.0 27.4 - - - -
75G SER* 4.9 5.9 + - - -
107G ASP* 3.9 13.3 - - - +
1160G LEU* 4.8 1.9 + - - +
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Residues in contact with ALA 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ILE* 4.3 6.5 - - + -
73E ARG 3.7 5.8 - - - -
74E VAL* 4.3 3.6 - - + +
124E VAL* 6.0 1.8 - - + -
128E LEU* 4.1 22.7 - - + -
129E LEU* 3.4 26.4 - - + +
134E VAL* 4.8 0.7 - - + -
136E ASP* 1.3 85.4 + - - +
138E GLN* 1.3 62.7 + - - +
104G GLY 4.2 0.2 - - - +
1160G LEU* 2.9 31.3 + - - +
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Residues in contact with GLN 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ILE* 4.1 0.8 - - - +
73E ARG* 2.6 87.3 + - - +
105E GLU* 5.8 2.2 + - - -
136E ASP* 5.8 0.4 - - - +
137E ALA* 1.3 77.9 - - - +
139E SER* 1.3 56.5 + - - +
105F GLU* 5.3 7.1 + - - +
104G GLY* 3.7 22.4 - - - +
105G GLU* 3.4 31.6 - - - +
1160G LEU 3.1 4.3 - - - -
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Residues in contact with SER 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E PHE 3.7 3.8 - - - -
72E ILE* 3.5 29.2 - - - -
73E ARG* 4.7 0.7 - - - -
120E PHE* 3.4 21.4 - - - -
124E VAL* 5.8 0.4 - - - -
138E GLN* 1.3 76.0 - - - +
140E SER* 1.3 63.8 + - - +
141E PHE* 4.0 4.6 - - - -
103F THR* 5.4 1.9 - - - +
103G THR* 3.7 20.4 + - - -
104G GLY* 4.1 5.0 + - - +
1160G LEU* 2.4 36.1 + - - -
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Residues in contact with SER 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ALA* 3.4 9.4 - - - +
71E PHE* 2.9 35.0 + - - +
73E ARG* 2.8 29.0 + - - +
139E SER* 1.3 72.6 + - - +
141E PHE* 1.3 68.1 + - - +
102F LEU* 4.5 16.2 - - - -
103F THR* 3.1 31.2 + - - -
104F GLY* 4.5 2.6 - - - -
106F THR* 6.0 0.5 - - - -
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Residues in contact with PHE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LEU* 3.5 39.0 - - + -
69E GLN 3.7 3.4 - - - +
70E ALA* 4.1 9.2 - - + +
117E MSE 3.3 27.1 - - + -
120E PHE* 3.6 38.6 - + - -
139E SER* 4.0 19.3 - - - -
140E SER* 1.3 82.0 - - - +
142E VAL* 1.3 64.6 + - - +
143E LEU* 3.4 1.9 + - - +
102F LEU* 3.5 5.2 - - - -
103F THR* 2.9 38.0 + - + +
103G THR* 4.0 16.2 - - + -
117H MSE 4.6 6.3 - - + -
141H PHE* 4.0 21.3 - + + -
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E GLY 5.5 2.9 - - - +
68E LEU* 5.6 1.7 - - - +
69E GLN* 3.0 52.0 + - + +
71E PHE* 5.0 0.4 - - + -
141E PHE* 1.3 70.2 - - - +
143E LEU* 1.3 63.4 + - - +
144E LYS 3.6 17.0 - - - +
145E GLU* 4.2 1.6 - - + +
100F PHE* 3.2 42.4 - - + -
101F ALA 4.1 0.4 - - - +
102F LEU* 3.5 13.5 - - + +
117H MSE 4.4 10.4 - - - +
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PHE 4.0 4.5 - - - +
142E VAL* 1.3 73.0 - - - +
144E LYS* 1.3 61.4 + - + +
101F ALA* 2.7 14.9 + - + +
102F LEU 4.0 4.0 - - - +
103F THR* 3.2 22.2 - - - +
1160F LEU* 3.4 47.6 - - + -
117H MSE 3.2 29.4 - - + -
120H PHE* 4.0 10.5 - - + -
121H SER* 2.7 32.3 + - - +
124H VAL* 4.0 5.2 - - + -
125H LEU* 3.8 16.8 - - + -
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Residues in contact with LYS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL* 3.4 7.2 - - - +
143E LEU* 1.3 82.6 - - - +
145E GLU* 1.3 64.8 + - - +
146E ILE* 3.4 24.2 + - + +
91F ARG* 6.3 1.1 - - - +
100F PHE* 3.5 3.1 - - - -
101F ALA* 2.9 39.2 + - + +
108F TYR* 5.7 1.8 - - - +
125H LEU* 4.1 21.0 - - + +
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Residues in contact with GLU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E PRO* 5.5 7.8 - - - +
69E GLN* 5.3 3.4 - - - +
142E VAL* 4.2 2.3 - - + +
144E LYS* 1.3 74.1 - - - +
146E ILE* 1.3 63.0 + - - +
147E LYS* 4.0 5.4 - - - +
148E HIS* 3.3 37.5 + - + +
53F ARG* 5.8 3.7 + - - -
91F ARG* 5.0 2.4 + - - -
99F CYS 3.9 2.7 - - - -
100F PHE* 3.6 27.5 - - + -
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Residues in contact with ILE 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LYS* 4.0 36.8 - - + +
145E GLU* 1.3 73.6 - - - +
147E LYS* 1.3 61.8 + - + +
86F PHE* 5.9 0.7 - - + -
87F ALA* 3.6 42.8 - - + +
90F VAL* 4.9 3.1 - - + -
91F ARG* 3.3 31.1 + - + +
99F CYS* 2.9 31.2 + - + +
108F TYR* 3.6 36.3 - - + +
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Residues in contact with LYS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLU* 3.3 6.8 - - - +
146E ILE* 1.3 85.5 - - + +
148E HIS* 1.3 67.2 + - - +
149E THR* 4.8 8.3 - - - +
90F VAL* 2.5 36.3 + - + +
91F ARG* 3.5 27.9 + - + +
93F TRP 2.8 24.5 + - - -
94F PRO* 4.4 2.0 - - - +
96F VAL 3.0 18.8 + - - +
97F LEU* 3.5 12.8 - - - +
98F SER* 3.7 1.0 - - - +
99F CYS* 2.7 41.7 + - + +
100F PHE* 4.4 0.7 - - - -
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Residues in contact with HIS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 6.3 0.4 - - - +
69E GLN* 5.8 1.3 - - - -
111E GLN* 5.2 9.4 - - - -
145E GLU* 3.3 32.0 + - + +
147E LYS* 1.3 78.8 - - - +
149E THR* 1.3 69.9 + - - +
150E THR* 4.7 12.7 - - + +
53F ARG* 3.6 32.7 + - - -
97F LEU 3.6 3.4 - - - -
98F SER* 3.7 17.0 - - - +
100F PHE* 3.8 14.3 - + + -
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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