Contacts of the strand formed by residues 132 - 138 (chain H) in PDB entry 1VQM
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 GLN 132 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46H GLN* 5.4 3.1 + - - -
48H SER* 2.8 33.4 + - - +
49H LEU 3.6 7.0 - - - -
50H ILE* 4.5 7.2 - - + +
88H ARG* 3.0 51.0 + - - +
89H LYS* 4.4 11.3 - - - -
127H VAL* 5.9 0.2 - - - -
130H GLY 5.2 2.0 - - - +
131H GLU* 1.3 74.1 - - - +
133H LEU* 1.3 60.0 + - - +
134H PHE 4.3 0.2 - - - +
135H THR* 3.2 10.6 + - - +
166H SER* 5.3 1.2 + - - -
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 2.8 14.9 + - + +
51H VAL* 4.5 13.9 - - + -
57H LEU* 3.8 25.6 - - + -
62H LEU* 4.2 8.1 - - + -
87H LEU* 3.5 19.7 - - + +
88H ARG* 3.2 27.9 + - - +
89H LYS* 3.9 21.3 - - + -
125H ALA* 6.2 0.2 - - + -
127H VAL* 4.2 6.7 - - + -
131H GLU 3.7 2.2 + - - -
132H GLN* 1.3 72.4 - - - +
134H PHE* 1.3 88.6 + - + +
157H ILE* 3.7 29.2 - - + -
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Residues in contact with PHE 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H MET* 5.6 0.2 - - + -
48H SER* 3.3 1.9 - - - -
49H LEU* 2.9 51.3 + - + +
62H LEU* 4.4 2.5 - - - -
65H SER* 3.3 29.4 - - - -
66H ARG* 3.6 38.6 - - + -
69H ALA* 5.6 1.1 - - + -
85H MET* 4.7 13.5 - - + -
86H THR 3.3 7.9 - - - +
87H LEU* 3.7 32.1 - - + -
88H ARG* 4.6 1.1 - - - -
132H GLN* 4.3 0.2 - - - +
133H LEU* 1.3 102.1 + - + +
135H THR* 1.3 68.7 + - - +
150H PHE* 3.9 21.1 - + + -
153H ALA* 4.6 5.4 - - + -
157H ILE* 5.5 0.2 - - + -
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Residues in contact with THR 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H GLN* 3.8 17.7 - - + +
47H ILE 3.5 5.6 - - - +
48H SER* 2.7 20.9 + - - +
85H MET* 3.5 1.8 - - - -
86H THR* 2.8 38.9 + - - -
88H ARG* 2.7 30.6 + - - +
132H GLN* 3.2 1.2 + - - +
134H PHE* 1.3 73.7 + - - +
136H ALA* 1.3 62.4 + - - +
137H TYR* 3.3 39.0 - - + +
150H PHE* 4.4 1.3 - - - -
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Residues in contact with ALA 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLN* 3.2 4.2 - - - -
47H ILE 2.8 32.2 + - - +
73H LEU* 5.1 3.8 - - + -
83H TYR* 6.0 0.7 - - + -
84H LYS 3.4 8.1 - - - +
85H MET* 4.2 12.6 - - + +
135H THR* 1.3 75.1 - - - +
137H TYR* 1.3 69.2 + - - +
138H CYS* 4.3 2.0 - - + -
146H VAL* 3.4 33.0 - - + -
150H PHE* 3.9 8.9 - - + -
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Residues in contact with TYR 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ALA* 3.4 38.5 - - + +
43H TYR* 3.5 20.7 - - + -
45H VAL 3.1 8.3 - - - +
46H GLN* 2.9 42.4 + - + -
83H TYR* 3.4 6.2 - - - +
84H LYS* 2.9 55.2 + - + -
86H THR* 4.3 13.3 + - - -
88H ARG* 4.5 6.8 + - - -
135H THR* 3.3 31.3 - - + +
136H ALA* 1.3 73.0 - - - +
138H CYS* 1.3 62.3 + - - +
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Residues in contact with CYS 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H TYR* 3.4 14.2 - - - +
44H PRO* 3.5 5.2 - - - +
45H VAL* 2.9 55.9 + - - +
47H ILE* 5.0 0.4 - - - -
77H LEU* 5.7 0.4 - - + -
82H ASP 4.6 1.8 - - - +
83H TYR* 4.5 10.5 - - + -
136H ALA* 5.6 1.3 - - + -
137H TYR* 1.3 76.3 - - - +
139H ASN* 1.3 71.4 + - - +
142H ASP* 3.6 27.1 - - + +
143H ALA* 3.6 7.4 - - - -
146H VAL* 3.9 15.0 - - + -
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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