Contacts of the strand formed by residues 105 - 110 (chain A) in PDB entry 2AQ5
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A HIS* 3.2 17.7 + - - -
100A GLY* 3.6 1.9 - - - -
101A SER 3.1 24.6 + - - -
103A ASP* 2.6 32.9 + - - +
104A CYS* 1.3 84.4 - - - +
106A VAL* 1.3 62.9 + - - +
107A MET* 3.6 8.7 - - + +
126A THR* 3.9 21.3 - - + -
127A LEU 3.6 8.7 - - - -
128A GLU* 4.2 15.9 - - + -
134A VAL* 4.2 1.6 - - - +
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 4.4 1.8 - - + -
99A SER 3.1 11.9 - - - +
105A THR* 1.3 77.4 - - - +
107A MET* 1.3 69.0 + - - +
126A THR* 3.5 2.1 - - - +
127A LEU* 2.7 62.5 + - + +
130A HIS* 4.9 2.7 - - + -
134A VAL* 3.8 17.7 - - + -
137A VAL* 4.0 12.8 - - + -
147A LEU* 3.9 17.9 - - + -
149A SER* 3.8 29.8 - - - +
159A TRP* 4.9 2.7 - - + +
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 3.9 19.3 - - - +
80A HIS* 3.5 30.9 - - + +
81A THR* 6.2 0.2 - - + -
98A ALA* 3.3 3.8 - - - +
99A SER* 2.9 32.5 + - - -
103A ASP* 4.1 2.9 - - - +
105A THR* 3.6 18.6 - - + +
106A VAL* 1.3 77.8 - - - +
108A VAL* 1.3 63.3 + - - +
109A TRP* 3.6 40.8 + - + +
123A PRO* 3.8 12.3 - - + -
125A ILE 3.5 3.1 - - - -
126A THR* 3.9 25.6 - - + +
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Residues in contact with VAL 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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96A VAL* 3.6 27.1 - - + -
97A ILE 3.6 4.3 - - - +
98A ALA* 4.4 2.5 - - + -
106A VAL* 4.8 0.4 - - + -
107A MET* 1.3 77.7 - - - +
109A TRP* 1.3 59.6 + - - +
123A PRO* 3.3 2.9 - - - +
124A VAL* 2.8 37.4 + - + +
125A ILE* 2.9 32.7 + - + -
127A LEU* 4.2 7.4 - - + -
139A TRP* 3.9 10.5 - - + -
147A LEU* 4.1 26.2 - - + -
161A VAL* 4.1 14.4 - - + -
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Residues in contact with TRP 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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59A PHE* 3.7 17.6 - + - -
77A VAL* 3.3 17.0 - - + -
78A CSO 3.2 34.3 - - - -
79A GLY* 3.8 8.7 - - - -
80A HIS* 4.5 1.3 - + - -
95A ASN 3.6 0.3 - - - +
96A VAL* 3.3 10.9 - - - +
97A ILE* 2.9 50.7 + - + +
99A SER* 2.9 23.2 + - - -
107A MET* 3.6 37.8 + - + +
108A VAL* 1.3 73.0 - - - +
110A GLU* 1.3 59.7 + - - +
111A ILE* 4.2 3.4 - - + -
120A LEU* 3.6 36.3 - - + -
121A ARG 3.9 1.3 - - - -
122A GLU 3.6 6.5 - - - -
123A PRO* 3.4 32.3 - - + -
124A VAL* 4.3 3.6 - - - +
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Residues in contact with GLU 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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93A ASN* 5.3 4.7 + - - -
95A ASN* 3.3 15.8 - - + +
96A VAL* 4.7 11.0 - - + +
109A TRP* 1.3 72.6 - - - +
111A ILE* 1.3 71.3 + - - +
112A PRO* 3.9 4.6 - - + +
120A LEU* 3.6 18.3 - - - +
124A VAL* 3.8 23.9 - - + +
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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