Contacts of the strand formed by residues 105 - 110 (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 THR 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.3 27.4 - - - +
103A ASN 4.6 3.1 - - - +
104A LEU* 1.3 76.1 - - - +
106A LEU* 1.3 61.5 + - - +
107A ARG* 3.9 8.6 + - - +
143A THR* 4.2 15.7 - - + -
145A THR* 3.4 29.6 - - + +
401A NAG 4.7 11.0 - - + -
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Residues in contact with LEU 106 (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* 4.6 11.2 - - + -
94A LEU* 5.2 5.4 - - + -
104A LEU* 4.1 6.3 + - + -
105A THR* 1.3 74.7 - - - +
107A ARG* 1.3 60.7 + - - +
123A LEU* 3.6 21.6 - - + +
124A LEU 5.3 2.9 - - - +
130A LEU* 5.0 4.3 - - + -
143A THR* 3.1 5.9 - - - +
144A THR* 3.1 44.1 + - + +
146A VAL* 3.4 27.6 - - + -
157A PHE* 3.4 45.1 - - + -
158A SER 6.0 0.2 - - - +
180A TYR* 4.6 14.4 - - + -
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Residues in contact with ARG 107 (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* 3.0 21.5 - - - +
92A ALA* 3.0 32.8 + - + +
94A LEU* 6.0 0.2 - - - +
105A THR* 3.9 9.8 + - - +
106A LEU* 1.3 73.9 - - - +
108A CYS* 1.3 66.6 + - - +
109A GLN* 5.2 9.2 + - + +
123A LEU* 4.6 0.7 - - - -
141A GLU* 3.2 41.0 + - - +
142A VAL 3.4 3.8 - - - +
143A THR* 3.0 32.8 + - + +
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Residues in contact with CYS 108 (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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89A VAL 3.2 17.9 - - - -
90A GLU 4.0 1.3 - - - -
91A LEU* 3.7 6.1 - - + +
92A ALA 4.6 0.4 - - - +
106A LEU 4.3 0.2 + - - -
107A ARG* 1.3 75.3 - - - +
109A GLN* 1.3 66.6 + - - +
110A VAL* 4.3 7.6 - - - -
123A LEU* 3.5 16.4 - - + -
140A ALA 3.1 11.8 - - - +
142A VAL* 2.9 30.2 + - + +
159A CYS* 2.0 50.9 - - + -
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Residues in contact with GLN 109 (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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88A ARG* 3.4 25.4 + - - +
89A VAL 3.4 4.6 - - - +
90A GLU 3.1 20.9 + - - +
91A LEU* 4.5 0.2 - - - +
92A ALA 5.3 0.6 - - - +
107A ARG* 5.2 9.4 + - + -
108A CYS* 1.3 82.7 - - - +
110A VAL* 1.3 64.7 + - - +
139A PRO* 3.6 37.3 - - + +
140A ALA 3.2 9.0 - - - +
141A GLU* 4.2 18.3 - - - +
142A VAL 5.0 0.4 - - - +
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Residues in contact with VAL 110 (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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86A PRO* 4.9 4.3 - - + -
88A ARG 3.3 5.8 - - - +
89A VAL* 4.0 11.4 - - + -
108A CYS* 4.3 9.2 - - - -
109A GLN* 1.3 79.9 - - - +
111A GLU* 1.3 60.2 + - - +
112A GLY 4.0 6.6 + - - +
116A ARG* 4.1 6.3 + - - +
119A LEU* 4.7 4.7 - - + -
121A VAL* 3.6 30.1 - - + -
135A ALA* 4.1 9.9 - - + -
139A PRO* 3.2 2.6 - - - +
140A ALA* 2.6 51.6 + - + +
161A THR* 3.9 21.5 - - + -
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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