Contacts of the strand formed by residues 138 - 145 (chain D) in PDB entry 2VRF
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 MET 138 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ARG 4.3 0.9 - - - -
138C MET* 4.4 9.4 - - + -
139C PRO* 3.6 18.2 - - + -
141C LEU* 4.6 12.6 - - + -
197C ILE* 4.3 19.7 - - - -
131D LYS* 5.0 9.0 - - + +
132D GLY* 4.0 14.8 - - - +
133D GLY* 3.1 33.2 + - - +
134D ARG* 3.8 2.3 + - - +
136D ASN* 3.8 19.5 - - + +
137D ARG* 1.3 82.8 - - - +
139D PRO* 1.3 68.8 - - + +
141D LEU* 3.7 28.5 - - + -
172D ARG 5.4 2.4 - - - +
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Residues in contact with PRO 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ASN 3.8 14.8 - - - +
137C ARG* 3.2 27.1 - - + +
138C MET* 3.6 13.7 - - + -
132D GLY* 3.3 17.3 - - - -
133D GLY 3.9 1.8 - - - -
138D MET* 1.3 92.3 - - + +
140D ILE* 1.3 62.9 + - - +
141D LEU* 3.3 26.0 + - + +
162D ALA* 4.1 17.7 - - + -
163D ILE 5.6 1.3 - - - +
164D LEU* 5.8 3.4 - - + -
171D LEU 5.7 1.3 - - - +
172D ARG* 5.3 9.6 - - - +
197D ILE* 4.3 5.2 - - + -
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Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 3.9 36.1 - - + -
131D LYS 3.5 3.1 - - - +
132D GLY 4.1 4.7 - - - +
133D GLY* 3.7 27.1 - - - +
139D PRO* 1.3 69.9 - - - +
141D LEU* 1.3 57.6 + - - +
162D ALA* 3.2 5.7 - - - +
163D ILE* 2.8 55.1 + - + +
171D LEU* 3.9 24.9 + - + +
174D ALA 4.0 7.6 - - - +
175D THR 4.3 2.5 - - - +
176D HIS* 4.4 2.2 - - - -
179D ALA* 3.4 29.6 - - + -
183D LEU* 4.7 2.5 - - + -
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C MET* 4.5 15.7 - - + -
130D ILE* 3.2 5.9 - - - -
131D LYS* 2.8 56.6 + - + +
138D MET* 3.7 27.6 - - + -
139D PRO* 3.6 31.0 - - + +
140D ILE* 1.3 73.6 - - - +
142D ILE* 1.3 64.9 + - - +
143D SER 3.3 0.5 + - - -
160D GLY* 4.6 8.1 - - - +
161D ASP 3.5 5.6 - - - +
162D ALA* 3.8 20.4 - - + +
163D ILE* 5.4 0.2 - - - -
197D ILE* 4.0 11.4 - - + -
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 4.0 20.6 - - + -
129D SER 3.6 5.8 - - - +
130D ILE* 4.6 0.4 - - - +
131D LYS* 5.2 1.0 - - - -
141D LEU* 1.3 72.1 - - - +
143D SER* 1.3 60.8 + - - +
144D LYS 3.7 20.4 - - - +
145D ILE* 3.7 18.8 - - + -
157D LEU* 4.0 33.7 - - + -
158D ARG 3.9 11.7 - - - +
159D LEU* 4.0 4.0 - - + +
160D GLY* 3.2 22.0 + - - -
161D ASP* 2.9 34.6 + - + +
163D ILE* 4.0 19.7 - - + -
192D LEU* 5.7 0.2 - - + -
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Residues in contact with SER 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLU* 5.2 0.9 - - - -
201C ASN* 2.7 30.4 + - - -
129D SER* 2.8 29.4 + - - -
130D ILE 3.7 2.8 - - - -
131D LYS* 3.9 23.6 - - - +
141D LEU 3.3 0.8 + - - -
142D ILE* 1.3 74.3 - - - +
144D LYS* 1.3 62.9 + - - +
159D LEU* 3.7 13.6 - - - +
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 3.1 10.6 - - - +
129D SER* 3.0 40.2 + - - +
142D ILE* 3.6 2.6 - - - +
143D SER* 1.3 81.0 - - - +
145D ILE* 1.3 73.6 + - - +
146D PHE* 3.6 38.8 - - + -
147D PRO* 5.1 6.7 - - - -
159D LEU* 3.5 5.8 - - + -
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLU* 3.8 18.6 - - - +
127D GLY 3.8 2.9 - - - +
128D ILE* 4.1 5.4 - - + -
142D ILE* 3.7 15.0 - - + -
144D LYS* 1.3 81.9 - - - +
146D PHE* 1.3 63.4 + - - +
147D PRO* 3.3 9.2 - - - +
151D ALA* 4.0 11.0 - - + -
152D ASP* 3.7 41.3 - - + +
157D LEU* 3.6 39.3 - - + +
158D ARG 3.8 12.6 - - - +
159D LEU* 3.6 9.8 - - + +
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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