Contacts of the strand formed by residues 129 - 143 (chain B) in PDB entry 5I7L
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 LEU 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.7 28.5 - - + -
120B LEU* 4.2 21.3 - - + -
121B VAL 3.5 15.0 - - - +
122B GLN* 3.7 22.0 - - + -
127B HIS 4.2 0.8 + - - -
128B ARG* 1.3 74.3 - - - +
130B TYR* 1.3 62.1 + - - +
162B GLU* 3.4 5.5 - - - +
163B ILE* 2.7 63.2 + - + +
175B LEU* 5.1 0.2 - - + -
242B ILE* 4.2 20.0 - - + -
246B LEU* 4.3 10.5 - - + -
252B PHE* 3.9 12.3 - - + -
253B CYS* 4.6 0.9 - - - -
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY 3.8 0.2 - - - +
120B LEU* 3.4 7.1 - - - +
121B VAL* 2.9 61.7 + - + +
122B GLN 4.9 0.4 - - - -
123B SER* 4.3 13.0 - - - -
128B ARG* 3.4 47.2 + - + -
129B LEU* 1.3 74.1 - - - +
131B VAL* 1.3 59.6 + - - +
160B THR* 4.8 13.7 - - + -
161B ALA 3.4 6.3 - - - +
162B GLU* 3.6 42.7 + - + -
163B ILE* 4.7 0.9 - - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 16.4 - - + -
118B LEU* 4.6 9.4 - - + -
119B GLY 3.2 11.7 - - - +
120B LEU* 3.5 18.4 - - + -
130B TYR* 1.3 75.0 - - - +
132B THR* 1.3 72.6 + - - +
133B ILE* 4.2 16.8 - - + -
159B ILE 3.5 0.9 - - - +
160B THR* 3.3 6.3 - - - +
161B ALA* 2.9 53.4 + - + +
163B ILE* 3.8 21.1 - - + +
227B VAL* 5.4 5.2 - - + -
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.5 6.2 - - - +
119B GLY* 3.0 36.5 + - - +
131B VAL* 1.3 73.6 - - - +
133B ILE* 1.3 65.2 + - - +
134B PRO* 3.2 12.3 - - + +
158B ASP* 3.9 32.5 - - + +
159B ILE 3.3 4.3 - - - +
160B THR* 3.4 16.6 + - - +
183B SER* 5.8 0.2 - - - -
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 6.5 0.4 - - + -
59B LEU* 3.8 17.3 - - + -
115B LEU* 3.5 27.4 - - + -
118B LEU* 3.6 11.0 - - + -
131B VAL* 4.4 15.7 - - + -
132B THR* 1.3 76.4 - - - +
134B PRO* 1.3 62.0 - - - +
135B LEU* 3.6 16.6 - - + +
157B LEU 3.6 1.9 - - - +
158B ASP* 3.3 3.6 - - - -
159B ILE* 2.7 57.1 + - + +
161B ALA* 5.9 1.1 - - + +
223B VAL* 4.8 3.1 - - + -
227B VAL* 3.5 37.7 - - + -
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Residues in contact with PRO 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.7 5.7 - - - +
116B LEU* 2.7 59.5 + - + +
117B GLU 3.2 25.8 - - - +
118B LEU* 3.9 8.7 - - + -
119B GLY 5.0 0.2 - - - +
132B THR* 3.2 17.3 - - + +
133B ILE* 1.3 82.5 - - - +
135B LEU* 1.3 58.0 + - - +
158B ASP* 3.2 21.1 - - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.7 35.4 - - + -
68B LEU* 3.8 20.9 - - + -
114B GLN 3.4 5.6 - - - +
115B LEU* 4.4 0.7 - - + -
116B LEU* 5.2 2.9 - - - +
133B ILE* 3.6 21.1 - - + +
134B PRO* 1.3 77.1 - - - +
136B GLY* 1.3 58.9 + - - +
155B VAL 3.8 0.2 - - - +
156B LYS* 3.4 9.2 - - - +
157B LEU* 2.9 40.4 + - + +
159B ILE* 3.5 32.5 - - + -
219B VAL* 3.8 18.6 - - + -
223B VAL* 4.5 5.8 - - + -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.3 1.0 - - - +
112B ASP 4.3 0.9 - - - -
113B PRO* 3.3 1.0 - - - +
114B GLN* 3.0 41.4 + - - +
116B LEU* 5.4 0.8 - - - +
135B LEU* 1.3 75.6 - - - +
137B ILE* 1.3 69.0 + - - +
155B VAL 3.2 9.6 - - - -
156B LYS* 4.0 19.3 - - - -
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.1 27.8 - - + -
71B LEU* 4.5 16.8 - - + -
73B LEU* 5.9 0.9 - - + -
110B VAL* 4.1 21.8 - - + -
111B THR 3.8 7.9 - - - +
112B ASP 3.9 3.1 - - - -
113B PRO* 4.2 6.5 - - + -
135B LEU* 6.2 0.2 - - + -
136B GLY* 1.3 79.7 - - - +
138B LYS* 1.3 59.6 + - - +
139B LEU* 4.1 21.8 - - + -
154B ALA* 3.7 1.7 - - - -
155B VAL* 2.7 59.5 + - + +
215B LEU* 4.7 12.6 - - + -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.6 5.0 - - - +
111B THR* 2.9 52.3 + - + +
112B ASP* 4.1 27.5 + - + +
114B GLN* 5.5 8.9 + - - +
137B ILE* 1.3 78.5 - - - +
139B LEU* 1.3 64.9 + - - +
152B ARG* 3.3 33.2 - - + +
153B LEU 3.2 5.4 - - - +
154B ALA* 4.3 10.0 - - - +
156B LYS* 5.8 3.4 - - - +
192B LEU* 3.6 24.9 - - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.9 22.4 - - + -
108B ILE* 4.1 14.6 - - + -
109B LYS 3.8 0.4 - - - -
110B VAL* 3.7 27.4 - - + -
111B THR* 5.3 0.4 - - - -
137B ILE* 4.1 11.0 - - + -
138B LYS* 1.3 80.6 - - - +
140B GLN* 1.3 61.5 + - - +
141B VAL* 3.9 5.0 + - + +
151B LEU 4.1 0.2 - - - +
152B ARG* 3.4 6.6 - - - +
153B LEU* 2.8 50.6 + - + +
155B VAL* 3.8 22.2 - - + -
211B LEU* 3.6 33.0 - - + -
215B LEU* 4.5 4.5 - - + -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP 3.3 1.4 - - - +
108B ILE* 3.0 8.7 - - - +
109B LYS* 2.9 75.2 + - + +
111B THR* 5.1 4.4 - - + +
138B LYS 4.1 0.4 - - - -
139B LEU* 1.3 72.2 - - - +
141B VAL* 1.3 60.3 + - - +
142B ASN* 2.9 31.0 + - - +
149B SER* 3.4 17.7 - - - -
151B LEU 3.0 20.9 + - - -
152B ARG* 3.1 37.8 - - + +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.1 26.2 - - + -
107B ASP 3.3 2.5 - - - +
108B ILE* 4.3 11.9 - - + +
139B LEU* 4.2 9.9 - - + +
140B GLN* 1.3 75.4 - - - +
142B ASN* 1.3 57.9 + - - +
150B LEU* 2.7 43.1 + - + +
151B LEU* 2.8 33.5 + - + +
153B LEU* 4.7 8.3 - - + -
203B LEU* 5.4 2.9 - - + -
207B LEU* 3.9 31.6 - - + -
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.3 7.4 - - - +
107B ASP* 2.6 57.7 + - + +
109B LYS* 4.5 11.7 - - - +
140B GLN* 2.9 41.6 + - - +
141B VAL* 1.3 74.5 - - - +
143B THR* 1.3 60.6 + - - +
144B PRO* 3.5 5.6 - - + -
148B ALA 3.5 10.1 - - - +
149B SER* 3.0 15.2 - - - -
150B LEU* 4.2 5.1 - - - +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 5.1 4.3 - - - +
100A PRO* 4.7 12.3 - - + +
105B ILE* 3.0 29.8 + - - +
142B ASN* 1.3 74.1 - - - +
144B PRO* 1.3 57.1 - - - +
145B LEU* 2.9 16.2 + - - +
146B VAL* 4.2 6.3 + - + +
147B GLY* 2.9 17.0 + - - -
148B ALA* 2.9 36.3 + - + +
150B LEU* 3.8 28.7 - - + -
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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
------------------------------------------------------------
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