Contacts of the strand formed by residues 138 - 148 (chain D) in PDB entry 1V8C
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 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C LEU* 3.8 23.6 - - + -
21C PRO* 4.7 2.2 - - + -
31C ASN* 3.6 32.3 - - + +
34C ARG* 4.0 28.7 - - + -
35C ALA* 3.6 13.4 - - + +
134D LYS* 3.4 7.6 - - - +
135D VAL* 2.8 42.9 + - + +
136D GLY 3.1 0.7 - - - +
137D SER* 1.3 80.0 - - - +
139D SER* 1.3 75.4 + - - +
140D ILE* 4.0 16.9 + - + +
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Residues in contact with SER 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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132D PRO* 3.7 24.4 - - - +
133D LEU 3.4 4.3 - - - -
134D LYS* 3.8 21.8 - - - +
137D SER 4.0 2.0 + - - -
138D LEU* 1.3 84.2 - - - +
140D ILE* 1.3 62.2 + - - +
141D PRO* 3.5 10.2 - - - +
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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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19C GLU 4.3 6.5 - - - +
20C LEU* 4.6 0.2 - - + -
21C PRO* 3.8 37.9 - - + -
94D GLY* 4.6 2.0 - - - -
95D ALA* 4.1 10.1 - - + +
132D PRO* 3.3 2.9 - - - +
133D LEU* 2.7 54.2 + - + +
135D VAL* 3.5 31.2 - - + -
138D LEU* 4.0 18.6 - - + +
139D SER* 1.3 76.1 - - - +
141D PRO* 1.3 71.1 - - + +
142D GLN* 3.4 15.5 + - - +
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Residues in contact with PRO 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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93D PHE 3.8 0.4 - - - +
94D GLY* 3.2 0.7 - - - -
95D ALA* 3.0 45.4 + - + +
96D PHE 4.7 3.6 - - - +
97D PRO* 5.4 11.2 - - + -
129D GLU* 4.5 14.6 - - - +
132D PRO* 3.9 9.8 - - + -
139D SER 3.5 10.1 - - - +
140D ILE* 1.3 85.8 - - + +
142D GLN* 1.3 68.8 + - - +
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Residues in contact with GLN 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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92D THR* 3.7 18.5 - - + +
93D PHE 3.4 2.0 - - - -
94D GLY* 3.6 15.5 + - - -
129D GLU* 3.4 9.8 + - - +
130D VAL* 3.0 49.6 + - + +
131D GLU 3.4 14.1 - - - +
132D PRO* 3.7 3.0 - - + +
133D LEU* 3.1 45.4 - - + +
140D ILE* 3.4 16.4 + - - +
141D PRO* 1.3 90.7 + - - +
143D LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 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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91D ARG 3.5 0.7 - - - +
92D THR* 3.3 2.7 - - - +
93D PHE* 2.7 39.8 + - + +
96D PHE* 3.2 35.7 - - + +
97D PRO 4.4 1.1 - - - -
98D PRO* 3.9 22.2 - - + -
101D LEU* 3.9 29.2 - - + -
127D PHE* 4.2 6.1 - - + -
128D ARG* 3.6 31.0 - - - +
129D GLU* 3.8 15.7 - - + +
142D GLN* 1.3 72.7 - - - +
144D ARG* 1.3 60.7 + - - +
145D VAL* 3.5 15.8 + - + +
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Residues in contact with ARG 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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90D GLU* 3.2 39.7 + - - +
91D ARG 3.7 3.8 - - - -
92D THR* 4.0 17.2 + - - +
126D ARG 3.9 0.2 - - - +
127D PHE* 3.0 6.8 - - - +
128D ARG* 2.9 79.0 + - + +
130D VAL* 4.0 15.2 - - + +
142D GLN 4.1 1.0 + - - -
143D LEU* 1.3 70.3 - - - +
145D VAL* 1.3 62.2 + - - +
146D GLU* 2.9 29.4 + - + +
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Residues in contact with VAL 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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89D PHE 4.1 0.2 - - - +
90D GLU* 3.0 6.6 - - - +
91D ARG 2.8 38.9 + - - +
93D PHE* 3.6 31.2 - - + -
96D PHE* 5.1 0.2 - - + -
101D LEU* 4.0 13.5 - - + -
125D VAL* 4.0 21.3 - - + -
126D ARG 3.3 7.0 - - - +
127D PHE* 3.9 12.1 - - + -
143D LEU* 3.8 10.5 - - + +
144D ARG* 1.3 77.6 - - - +
146D GLU* 1.3 67.2 + - - +
147D VAL* 4.3 5.6 - - + -
156D PHE* 4.8 3.3 - - + -
159D ILE* 4.1 17.5 - - + -
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Residues in contact with GLU 146 (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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89D PHE 3.4 4.0 - - - -
90D GLU* 3.6 15.0 - - + -
124D VAL 3.6 1.0 - - - +
125D VAL* 3.4 3.6 - - - +
126D ARG* 2.6 62.3 + - + +
128D ARG* 5.0 4.4 + - - -
144D ARG* 2.9 37.2 + - + +
145D VAL* 1.3 79.6 - - - +
147D VAL* 1.3 63.3 + - - +
148D GLU* 3.4 16.9 - - - +
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Residues in contact with VAL 147 (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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88D GLY* 3.3 1.9 - - - -
89D PHE 2.8 36.4 + - - +
123D ALA* 4.1 13.0 - - + -
124D VAL 3.4 7.4 - - - +
125D VAL* 4.3 7.2 - - + -
145D VAL* 4.3 4.5 - - + -
146D GLU* 1.3 79.1 - - - +
148D GLU* 1.3 66.5 + - - +
152D ALA* 3.6 35.7 - - - +
155D TRP* 4.3 9.0 - - + -
156D PHE* 4.1 21.5 - - + -
159D ILE* 4.0 26.7 - - + -
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Residues in contact with GLU 148 (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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87D GLY 3.4 13.9 - - - +
88D GLY* 4.4 5.1 - - - -
89D PHE 4.2 4.0 + - - +
123D ALA* 3.0 4.7 - - - +
124D VAL* 2.8 40.4 + - + +
126D ARG* 2.6 36.1 + - - +
146D GLU* 3.4 21.0 - - - +
147D VAL* 1.3 96.6 + - - +
149D GLY* 1.3 60.7 + - - +
152D ALA* 3.8 4.3 - - - -
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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