Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 1QXR
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 GLU 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A HIS* 3.0 8.0 + - + -
96A ALA* 1.3 76.4 - - - +
98A VAL* 1.3 71.6 + - - +
99A TYR* 3.6 17.0 - - + -
129A TYR* 3.8 2.1 - - - -
130A VAL* 2.8 47.1 + - + +
150A ALA* 3.5 6.9 - - - +
151A ILE 3.4 14.1 - - - +
152A TYR* 3.4 16.7 - - + +
200A NI 2.2 37.7 - - - +
300A PA5 2.5 31.3 - - - +
66B LEU* 3.8 2.9 - - - -
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Residues in contact with VAL 98 (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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97A GLU* 1.3 78.4 - - - +
99A TYR* 1.3 65.8 + - - +
100A VAL* 4.5 5.6 - - + -
127A VAL* 3.7 24.7 - - + -
128A VAL 3.4 3.8 - - - +
129A TYR* 4.6 8.3 - - + -
150A ALA* 3.4 1.6 - - - -
151A ILE* 2.8 37.4 + - + +
66B LEU* 4.2 14.8 - - + +
68B PHE* 3.9 25.6 - - + -
149B LEU* 5.9 0.7 - - + -
151B ILE* 4.1 39.7 - - + -
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Residues in contact with TYR 99 (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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97A GLU* 3.6 24.2 - - + -
98A VAL* 1.3 75.5 - - - +
100A VAL* 1.3 64.6 + - - +
101A ALA 4.1 0.4 - - - -
108A MET* 3.4 34.5 - - + -
122A MET* 4.2 11.2 - - + -
127A VAL* 3.0 9.4 - - - +
128A VAL* 2.8 37.0 + - + +
130A VAL* 3.9 13.2 - - + -
136A HIS* 3.3 14.7 - + - -
138A THR* 3.9 9.7 + - + +
148A PHE* 3.2 47.6 - + - -
149A LEU 3.3 3.8 - - - -
150A ALA* 4.1 9.6 - - + -
300A PA5 3.0 28.9 + - - -
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Residues in contact with VAL 100 (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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98A VAL* 4.5 4.9 - - + -
99A TYR* 1.3 78.5 - - - +
101A ALA* 1.3 63.6 + - - +
102A LEU* 3.6 9.9 + - + +
125A GLY 5.4 0.4 - - - +
126A THR 3.6 2.9 - - - +
127A VAL* 4.1 15.9 - - + -
148A PHE* 3.2 5.1 - - - -
149A LEU* 2.8 51.9 + - + +
151A ILE* 4.3 16.6 - - + -
12B PHE* 4.0 26.2 - - + -
100B VAL* 5.8 1.8 - - + -
149B LEU* 3.7 28.5 - - + -
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Residues in contact with ALA 101 (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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99A TYR 4.1 0.4 - - - -
100A VAL* 1.3 75.2 - - - +
102A LEU* 1.3 64.1 + - - +
103A LYS 5.2 0.4 - - - +
122A MET* 3.9 26.5 - - + +
123A GLU 3.2 28.7 - - - +
124A PRO* 4.2 0.2 - - + -
125A GLY* 2.9 25.3 + - - -
126A THR 2.9 15.2 + - - +
146A PHE* 4.4 8.7 - - + -
148A PHE* 4.0 7.6 - - - -
12B PHE* 4.2 1.9 - - - -
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Residues in contact with LEU 102 (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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10A VAL* 4.6 3.6 - - + -
11A ASP 5.2 0.4 - - - +
12A PHE* 3.9 61.2 - - + +
13A GLU* 5.8 0.2 - - - +
15A GLY* 5.4 0.2 - - - -
70A THR* 4.6 8.3 - - + -
100A VAL* 3.9 24.5 - - + +
101A ALA* 1.3 80.5 - - - +
103A LYS* 1.3 64.6 + - - +
124A PRO* 3.5 17.4 - - - +
147A ILE* 2.8 22.8 + - + +
148A PHE* 4.3 4.3 - - - -
149A LEU* 4.3 22.7 - - + +
12B PHE* 4.3 15.4 - - + -
100B VAL* 6.2 0.7 - - + -
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Residues in contact with LYS 103 (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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12A PHE 4.0 13.7 - - - +
13A GLU* 2.8 51.8 + - - +
101A ALA* 3.9 0.8 - - - +
102A LEU* 1.3 80.7 - - - +
104A GLY* 1.3 69.8 + - - +
124A PRO* 4.0 6.2 - - + +
144A GLU* 6.3 3.8 - - + -
145A PRO* 4.0 9.6 - - + +
146A PHE* 3.3 8.4 - - - -
147A ILE* 2.9 42.6 + - + -
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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