Contacts of the strand formed by residues 134 - 144 (chain E) in PDB entry 3VI4
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 GLY 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E GLN* 3.0 36.1 + - - +
130E LEU* 3.7 8.7 + - - +
132E SER* 3.6 4.2 + - - -
133E GLY* 1.3 80.9 - - - +
135E ALA* 1.3 62.0 + - - +
185E THR* 6.3 0.9 - - - -
186E LEU 4.0 6.3 - - - -
187E THR* 4.7 0.7 - - - -
188E LYS 4.1 2.7 - - - -
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Residues in contact with ALA 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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125E PRO* 3.9 9.9 - - + -
129E GLN* 3.7 2.4 + - - -
130E LEU* 4.2 4.9 - - + -
134E GLY* 1.3 74.3 - - - +
136E SER* 1.3 62.6 + - - +
137E VAL* 4.2 2.0 + - - +
184E LEU 3.7 1.6 - - - +
185E THR* 3.5 3.0 - - - +
186E LEU* 2.9 43.8 + - + +
188E LYS* 4.2 3.8 - - - -
191E TYR* 3.5 45.3 - - + -
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Residues in contact with SER 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO 3.9 1.9 - - - +
125E PRO* 3.3 24.8 - - - +
129E GLN* 3.1 31.1 + - - +
135E ALA* 1.3 69.9 - - - +
137E VAL* 1.3 63.2 + - - +
138E VAL* 4.0 6.4 + - - +
183E THR* 4.0 9.4 - - - +
184E LEU 3.4 4.7 - - - -
185E THR* 3.2 28.9 + - - +
129F LEU* 5.5 1.4 - - - +
146F LEU* 3.8 16.1 - - - +
148F LYS* 4.1 6.9 - - - -
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Residues in contact with VAL 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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122E ILE* 3.9 15.5 - - + -
123E PHE 3.4 15.5 - - - +
124E PRO* 4.9 2.5 - - + -
125E PRO* 3.9 16.8 - - + -
135E ALA 5.1 1.3 - - - +
136E SER* 1.3 75.9 - - - +
138E VAL* 1.3 61.0 + - - +
153E TRP* 3.6 31.8 - - + -
183E THR* 3.5 3.8 - - - -
184E LEU* 2.9 38.6 + - + +
186E LEU* 6.1 1.3 - - + -
191E TYR* 4.3 14.6 - - + -
197E TYR* 4.3 22.7 - - + -
214E PHE* 5.3 4.3 - - + -
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ILE* 3.3 5.9 - - - +
123E PHE* 2.8 39.9 + - + -
136E SER 4.5 4.0 - - - +
137E VAL* 1.3 75.7 - - - +
139E CYS* 1.3 63.5 + - - +
140E PHE* 3.8 35.7 - - + -
181E SER* 4.4 3.1 - - - +
182E SER 3.7 2.5 - - - +
183E THR* 3.9 20.2 - - + +
129F LEU* 3.8 34.5 - - + -
146F LEU* 4.5 20.0 - - + -
183F SER* 4.0 6.1 - - - +
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Residues in contact with CYS 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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120E VAL* 3.8 8.3 - - - -
121E SER 3.2 5.8 - - - -
138E VAL* 1.3 76.0 - - - +
140E PHE* 1.3 63.6 + - - +
141E LEU* 3.6 25.9 + - - +
151E VAL* 5.2 0.7 - - - -
153E TRP* 3.7 11.4 - - + -
181E SER* 3.8 0.7 - - - -
182E SER* 2.8 44.4 + - - +
199E CYS* 2.0 48.5 - - - -
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E THR 3.4 2.3 - - - +
120E VAL* 3.3 5.0 - - - -
121E SER* 3.1 32.5 + - - +
123E PHE* 3.3 36.3 - + + -
138E VAL* 3.8 6.3 - - + -
139E CYS* 1.3 71.4 - - - +
141E LEU* 1.3 61.7 + - - +
142E ASN* 3.6 18.6 - - - +
180E MET 3.7 2.5 - - - -
181E SER* 3.5 24.5 - - - -
129F LEU* 3.8 27.8 - - + -
142F THR* 4.4 2.2 - - + -
144F GLY* 4.2 3.1 - - - -
171F PHE* 3.5 24.7 - + - -
183F SER* 3.5 10.3 - - - -
184F SER 3.8 4.9 - - - -
185F SER* 3.6 35.4 - - - -
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Residues in contact with LEU 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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118E PRO* 4.1 9.2 - - + -
119E THR 4.0 3.4 - - - -
120E VAL* 3.5 27.8 - - + -
139E CYS* 3.6 17.7 - - - +
140E PHE* 1.3 80.2 - - - +
142E ASN* 1.3 60.9 + - - +
144E PHE* 3.0 19.8 - - + -
149E ILE* 3.4 25.8 - - + -
151E VAL* 3.6 30.7 - - + -
179E SER* 3.4 0.2 - - - -
180E MET* 2.8 51.9 + - + +
182E SER* 5.9 1.1 - - - -
199E CYS* 5.6 0.2 - - + -
201E ALA* 3.7 12.1 - - + -
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Residues in contact with ASN 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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119E THR* 3.5 27.2 + - - +
121E SER* 5.5 0.4 + - - -
140E PHE* 3.6 19.5 - - - +
141E LEU* 1.3 76.2 - - - +
143E ASN* 1.3 74.0 + - - +
144E PHE* 3.8 2.1 - - - -
177E THR* 4.7 0.2 + - - -
178E TYR 2.6 15.7 - - - +
179E SER* 2.1 31.2 + - - -
142F THR* 4.5 12.3 + - - +
169F HIS* 3.9 13.1 + - - -
171F PHE* 4.3 7.4 - - - -
185F SER* 3.4 23.9 + - - -
187F THR* 4.5 12.3 + - - +
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Residues in contact with ASN 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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116E ALA* 3.7 11.1 - - - +
117E ALA 3.7 13.9 - - - +
119E THR* 4.2 17.6 + - - +
142E ASN* 1.3 84.6 - - - +
144E PHE* 1.3 59.9 + - - +
175E ASP* 5.5 2.8 - - - +
177E THR* 3.7 26.7 + - + +
178E TYR 3.6 1.6 - - - -
169F HIS* 3.0 33.8 + - - -
187F THR* 5.7 2.6 + - - -
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Residues in contact with PHE 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ALA* 3.3 19.5 - - - +
118E PRO* 3.7 26.7 - - + -
141E LEU* 3.0 33.0 - - + -
143E ASN* 1.3 82.9 - - - +
145E TYR* 1.3 62.5 + - - +
146E PRO 3.6 15.5 - - - -
147E LYS* 5.0 0.7 - - - -
148E ASP 4.6 3.4 - - - -
149E ILE* 3.8 33.9 - - + -
168E TRP* 5.8 1.8 - + - -
177E THR* 3.5 6.2 - - - -
178E TYR* 3.0 57.3 + - + -
179E SER* 3.8 9.4 - - - -
180E MET* 4.0 10.1 - - + -
203E HIS* 4.0 4.9 - - + -
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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