Contacts of the strand formed by residues 135 - 142 (chain A) in PDB entry 2V5Y
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 TYR 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLN* 3.4 5.4 - - - -
69A LEU* 3.0 51.8 + - + +
71A GLU* 6.0 0.2 - - + -
75A HIS* 2.8 33.6 + + - -
77A ILE* 3.5 17.2 - - + +
98A VAL* 4.0 15.9 - - + -
99A LYS 3.2 11.7 - - - +
100A VAL* 4.1 7.6 - - + +
127A ILE* 3.2 48.5 - - + +
129A THR* 3.5 28.9 - - + -
134A PHE* 1.3 77.1 - - - +
136A GLN* 1.3 62.3 + - - +
137A VAL* 3.8 15.9 - - + -
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 5.1 3.2 + - - -
65A LEU* 3.2 31.0 - - + +
66A LEU 2.8 28.0 + - - +
67A PRO* 4.4 5.8 - - - +
68A GLN* 4.1 31.2 + - + +
97A TYR 3.7 0.5 - - - +
98A VAL* 3.5 2.3 - - - -
99A LYS* 2.7 54.2 + - + +
135A TYR* 1.3 76.0 - - - +
137A VAL* 1.3 69.0 + - - +
138A ILE* 3.8 12.3 + - + +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.6 0.3 - - - -
66A LEU* 3.0 47.1 + - + +
67A PRO 4.8 0.8 + - - -
69A LEU* 5.2 0.9 - - + +
77A ILE* 3.5 32.5 - - + -
96A VAL* 3.7 25.8 - - + -
97A TYR 3.5 4.0 - - - +
98A VAL* 4.5 2.9 - - + +
125A LEU* 4.5 7.4 - - + -
127A ILE* 3.9 8.3 - - + -
135A TYR* 3.8 15.3 - - + -
136A GLN* 1.3 73.8 - - - +
138A ILE* 1.3 68.0 + - - +
139A PHE* 4.2 20.0 - - + -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A HIS* 3.9 26.2 - - + +
64A LEU 3.7 4.9 - - - +
65A LEU* 3.5 35.4 - - + -
95A ASN 3.6 0.2 - - - +
96A VAL* 3.2 6.7 - - - +
97A TYR* 2.9 46.0 + - + +
99A LYS* 4.5 15.9 - - + +
105A LEU* 3.8 22.0 - - + -
136A GLN* 3.8 20.2 - - + +
137A VAL* 1.3 82.0 - - - +
139A PHE* 1.3 70.9 + - - +
140A GLU 3.8 0.5 + - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 5.8 0.7 - + - -
28A TRP* 3.8 19.9 + - + -
62A ALA 3.7 1.0 - - - +
63A HIS* 3.5 3.5 - - - -
64A LEU* 2.9 49.5 + - + +
66A LEU* 3.6 28.7 - - + -
77A ILE* 6.3 1.6 - - + -
79A PHE* 3.6 52.0 - + + -
94A LEU* 4.6 6.5 - - + -
95A ASN 3.5 1.1 - - - -
96A VAL* 3.7 23.1 - - + -
125A LEU* 5.8 0.4 - - + -
137A VAL* 4.2 11.4 - - + -
138A ILE* 1.3 74.7 - - - +
140A GLU* 1.3 60.3 + - - +
152A ILE* 4.2 22.7 - - + -
155A VAL* 4.4 12.1 - - + -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ARG* 3.4 19.1 + - + -
62A ALA 3.4 3.8 - - - -
63A HIS* 2.9 38.3 + - + +
94A LEU* 3.3 5.1 - - - +
95A ASN* 2.6 61.0 + - - +
97A TYR* 2.5 45.3 + - + -
105A LEU* 5.2 0.5 - - - +
138A ILE 3.8 0.4 + - - -
139A PHE* 1.3 74.3 - - - +
141A VAL* 1.3 74.1 + - - +
142A ILE* 3.8 13.7 + - + +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 5.1 0.6 - - + -
28A TRP* 3.6 28.7 - - + -
51A VAL* 3.7 31.9 - - + -
53A ALA* 5.7 0.4 - - + -
60A GLN 4.1 0.2 - - - +
61A ARG* 3.2 7.1 - - - +
62A ALA* 3.1 31.7 + - + +
92A GLY* 4.6 0.7 - - - -
93A LEU 3.1 10.8 - - - +
94A LEU* 3.9 11.2 - - + -
140A GLU* 1.3 73.9 - - - +
142A ILE* 1.3 71.8 + - - +
143A THR* 4.3 7.2 - - + +
150A LEU* 3.6 29.4 - - + -
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 5.1 2.5 - - - +
59A GLY* 3.7 24.7 - - - +
60A GLN 3.7 2.9 - - - -
61A ARG* 3.8 31.4 - - + +
92A GLY* 3.0 4.6 - - - -
93A LEU* 2.8 53.8 + - + +
95A ASN* 3.9 14.1 - - - +
97A TYR* 5.2 0.4 - - - +
140A GLU* 3.8 26.9 + - - +
141A VAL* 1.3 77.2 - - - +
143A THR* 1.3 70.9 + - - +
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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