Contacts of the strand formed by residues 128 - 138 (chain M) in PDB entry 1V7M
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 128 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123M GLN* 3.2 32.5 + - - +
124M LEU* 3.2 19.4 - - - +
126M SER* 3.5 2.4 + - - -
127M GLY* 1.3 79.2 - - - +
129M ALA* 1.3 61.4 + - - -
180M LEU 3.8 4.7 - - - -
181M THR* 4.9 0.2 - - - -
182M LYS 3.9 3.8 - - - -
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Residues in contact with ALA 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M PRO* 4.0 5.8 - - + -
123M GLN* 3.3 6.0 + - - +
124M LEU* 3.9 6.5 - - + -
128M GLY* 1.3 76.4 - - - +
130M SER* 1.3 63.1 + - - +
131M VAL* 4.1 1.4 + - - +
178M LEU 3.8 1.4 - - - +
179M THR* 3.7 1.4 + - - -
180M LEU* 3.0 41.0 + - - +
181M THR 4.2 2.9 - - - +
182M LYS* 4.3 0.2 - - - -
185M TYR* 3.5 43.1 - - + -
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Residues in contact with SER 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I LEU* 5.5 1.4 - - - +
144I LEU* 4.0 15.0 - - - +
146I LYS* 4.1 7.1 + - - -
117M PHE 4.1 0.9 - - - +
118M PRO 4.1 1.0 - - - -
119M PRO* 3.3 23.4 - - - +
123M GLN* 2.6 39.2 + - - +
129M ALA* 1.3 73.5 - - - +
131M VAL* 1.3 61.7 + - - +
132M VAL* 4.1 4.6 + - - +
177M THR* 3.8 17.6 - - - +
178M LEU 3.2 4.3 - - - -
179M THR* 3.5 25.0 + - - +
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Residues in contact with VAL 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M ILE* 4.1 5.6 - - + -
117M PHE 3.4 16.2 - - - +
119M PRO* 4.1 15.3 - - + -
129M ALA 4.8 2.9 - - - +
130M SER* 1.3 75.8 - - - +
132M VAL* 1.3 59.9 + - - +
147M TRP* 3.2 32.1 - - + -
177M THR* 3.3 2.2 - - - -
178M LEU* 2.7 44.6 + - + +
180M LEU* 5.1 3.1 - - + -
185M TYR* 4.4 12.1 - - + -
191M TYR* 4.4 13.5 - - + -
208M PHE* 3.5 30.1 - - + -
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Residues in contact with VAL 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I LEU* 3.4 39.3 - - + -
144I LEU* 5.5 7.6 - - + -
181I SER* 5.1 3.1 - - - +
116M ILE* 3.5 1.7 - - - +
117M PHE* 2.8 43.3 + - + +
130M SER* 4.8 4.0 - - - +
131M VAL* 1.3 74.3 - - - +
133M CYS* 1.3 65.8 + - - +
134M PHE* 3.9 37.5 - - + -
147M TRP* 4.3 0.9 - - - -
175M SER* 4.4 4.0 - - - +
176M SER 3.3 7.9 - - - +
177M THR* 4.2 13.7 - - + +
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Residues in contact with CYS 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M VAL* 3.8 15.0 - - - -
115M SER 3.1 14.6 - - - -
116M ILE* 4.4 2.9 - - - -
132M VAL* 1.3 75.1 - - - +
134M PHE* 1.3 60.2 + - - +
135M LEU* 3.6 7.6 - - + +
147M TRP* 3.7 17.0 - - + -
175M SER* 3.8 2.3 + - - -
176M SER* 2.8 34.6 + - - +
193M CYS* 2.0 51.6 - - - -
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Residues in contact with PHE 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I LEU* 4.3 12.3 - - + -
140I THR* 4.5 1.6 - - + -
141I LEU 4.2 7.4 - - - -
169I PHE* 3.4 28.3 - + - -
181I SER* 3.4 10.8 - - - -
182I SER 3.7 13.2 - - - -
183I SER* 3.6 25.1 - - - -
113M THR 3.3 1.5 - - - +
114M VAL* 3.2 6.9 - - - +
115M SER* 2.9 39.3 + - - +
117M PHE* 3.3 33.4 - + - -
132M VAL* 3.9 16.8 - - + -
133M CYS* 1.3 73.7 - - - +
135M LEU* 1.3 60.2 + - - +
136M ASN* 3.9 13.9 - - - +
174M MET 3.8 0.9 - - - -
175M SER* 3.1 26.5 - - - -
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Residues in contact with LEU 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M PRO* 4.1 10.8 - - + -
113M THR 3.5 5.6 - - - -
114M VAL* 4.4 12.1 - - + -
133M CYS* 3.6 26.9 - - + +
134M PHE* 1.3 78.3 - - - +
136M ASN* 1.3 60.4 + - - +
138M PHE* 3.1 15.5 - - + -
143M ILE* 3.5 24.9 - - + -
145M VAL* 3.9 21.5 - - + -
174M MET* 2.9 53.7 + - + +
176M SER* 4.7 2.5 - - - -
193M CYS* 4.8 1.8 - - - -
195M ALA* 3.5 20.9 - - + -
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Residues in contact with ASN 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I THR* 5.1 3.8 - - - +
167I HIS* 3.6 13.5 - - + -
169I PHE* 3.6 10.0 - - - -
183I SER* 3.3 25.7 + - - -
185I THR* 5.0 7.7 + - - -
112M PRO* 3.7 0.2 - - - +
113M THR* 2.8 51.3 + - + +
134M PHE* 3.9 14.1 - - - +
135M LEU* 1.3 84.8 + - - +
137M ASN* 1.3 74.7 + - - +
138M PHE* 3.7 2.0 - - - -
173M SER* 3.0 17.7 + - - -
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Residues in contact with ASN 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I HIS* 2.7 35.4 + - - -
110M ALA* 4.0 5.5 - - - +
111M ALA 3.4 13.5 - - - +
113M THR* 4.9 4.3 + - - +
136M ASN* 1.3 77.4 - - - +
138M PHE* 1.3 59.0 + - - +
166M ASP* 4.9 3.4 + - - -
169M ASP* 3.0 25.7 + - - +
171M THR* 3.3 29.4 + - + +
172M TYR 3.2 2.6 + - - -
173M SER* 3.0 9.6 + - - -
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Residues in contact with PHE 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M ALA* 3.3 16.2 - - - +
112M PRO* 3.5 31.6 - - + -
135M LEU* 3.1 30.3 - - + -
137M ASN* 1.3 74.6 - - - +
139M TYR* 1.3 63.7 + - - +
140M PRO 3.2 20.4 - - - -
141M LYS* 3.4 29.6 - - - -
143M ILE* 4.1 21.1 - - + -
162M TRP* 4.3 2.5 - - - -
171M THR* 3.4 4.0 - - - -
172M TYR* 2.7 56.5 + - + +
173M SER* 3.6 13.7 - - - -
174M MET* 3.7 11.2 - - + -
197M HIS* 3.8 8.5 - + - +
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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