Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 1MQ8
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A PRO* 4.5 14.1 - - + -
110A VAL* 4.7 6.7 - - + -
112A GLY 3.5 12.8 - - - +
113A GLY* 3.8 10.1 - - - -
115A PRO 3.4 6.3 + - - +
116A ARG* 3.4 41.1 + - - +
117A ALA 5.3 0.5 - - - -
118A ASN* 1.3 76.5 - - - +
120A THR* 1.3 62.5 + - - +
121A VAL* 5.4 0.4 - - + -
134A PRO* 3.7 4.9 - - - +
135A ALA* 3.2 31.9 + - + +
161A THR* 4.1 26.0 - - + +
162A GLU 3.6 2.5 - - - -
163A LEU* 3.6 34.1 - - + +
173A PHE 5.1 0.4 - - - +
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Residues in contact with THR 120 (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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118A ASN 3.6 6.3 + - - +
119A LEU* 1.3 77.3 - - - +
121A VAL* 1.3 67.7 + - - +
122A VAL* 5.5 1.0 - - - +
132A ARG* 4.1 22.1 + - + +
133A GLU* 3.8 7.4 - - - -
134A PRO* 4.2 20.0 - - + -
161A THR* 3.4 5.2 - - - -
162A GLU* 2.9 50.7 + - - +
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Residues in contact with VAL 121 (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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110A VAL* 3.6 35.9 - - + -
119A LEU* 5.4 1.1 - - + -
120A THR* 1.3 81.0 - - - +
122A VAL* 1.3 66.3 + - - +
131A LYS 3.5 0.7 - - - +
132A ARG* 3.1 3.6 - - - +
133A GLU 2.6 47.7 + - - +
135A ALA* 4.2 14.1 - - + -
140A ALA* 5.0 2.7 - - + -
142A VAL* 4.0 32.6 - - + +
159A CYS* 4.0 14.1 - - - -
160A ARG 3.7 8.7 - - - +
161A THR* 4.4 5.2 - - + -
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Residues in contact with VAL 122 (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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120A THR* 5.5 0.9 - - - +
121A VAL* 1.3 83.8 - - - +
123A LEU* 1.3 75.5 + - - +
124A LEU* 3.4 11.7 - - + +
129A GLU* 4.6 7.9 - - + -
130A LEU 4.5 4.3 - - - +
131A LYS 2.9 15.3 - - - +
132A ARG* 3.6 23.6 - - + +
159A CYS* 3.7 1.2 - - - -
160A ARG* 3.1 56.1 + - + +
162A GLU* 4.3 20.2 - - + +
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Residues in contact with LEU 123 (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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91A LEU* 4.2 15.7 - - + -
106A LEU* 3.6 33.0 - - + +
108A CYS* 3.5 24.9 - - + +
121A VAL* 4.9 0.2 - - - +
122A VAL* 1.3 74.3 - - - +
124A LEU* 1.3 62.7 + - - +
130A LEU* 2.9 26.6 + - + +
131A LYS* 2.9 15.1 + - + +
142A VAL* 3.6 32.7 - - + +
143A THR* 3.9 6.7 - - - +
144A THR* 3.7 27.8 - - + -
158A SER 3.9 3.6 - - - +
159A CYS* 4.2 9.0 - - + -
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Residues in contact with LEU 124 (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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106A LEU* 5.3 2.0 - - - +
122A VAL* 3.4 26.0 - - + +
123A LEU* 1.3 75.9 - - - +
125A ARG* 1.3 54.8 + - - +
126A GLY 3.3 19.1 + - - +
127A GLU* 4.8 6.3 - - - +
128A LYS 2.9 26.0 - - - +
129A GLU* 4.4 2.5 - - - -
130A LEU* 3.7 7.8 - - - +
157A PHE* 3.5 4.4 - - - +
158A SER* 2.8 65.3 + - - +
159A CYS* 4.2 1.8 - - - +
160A ARG* 4.0 33.9 - - + +
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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