Contacts of the strand formed by residues 124 - 131 (chain A) in PDB entry 1RQ7
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ASP 2.8 16.7 + - - +
95A MET* 3.3 41.3 - - + +
96A VAL 2.7 31.2 + - - +
122A GLY 3.8 1.8 + - - -
123A ALA* 1.3 69.1 - - - +
125A THR* 1.3 54.4 + - - +
126A VAL* 3.8 4.9 + - + -
156A ASP* 3.5 26.7 - - + +
208A PHE* 4.1 12.3 - - + -
211A VAL* 4.2 6.5 - - + +
212A LYS* 3.7 33.7 - - + +
215A MET* 4.2 6.3 - - + -
216A SER* 3.7 30.1 - - - +
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Residues in contact with THR 125 (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 3.5 7.6 - - - +
98A VAL* 4.8 5.2 - - + -
115A ALA* 3.7 36.8 - - + +
118A ALA* 3.4 11.0 - - + +
119A ARG* 3.3 20.6 + - - -
123A ALA 3.0 12.4 + - - -
124A LEU* 1.3 70.4 - - - +
126A VAL* 1.3 63.0 + - - +
154A SER 4.0 9.2 - - - +
155A CYS* 4.1 6.1 - - - -
156A ASP* 2.7 50.8 + - - +
157A THR 3.3 2.1 + - - +
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Residues in contact with VAL 126 (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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95A MET* 4.0 26.7 - - + -
96A VAL 2.9 10.6 + - - +
97A PHE* 3.1 33.3 - - + +
98A VAL 3.0 23.2 + - - -
124A LEU* 4.3 12.6 - - + +
125A THR* 1.3 76.6 - - - +
127A GLY* 1.3 72.5 + - - +
128A VAL* 4.0 4.5 - - + -
155A CYS* 4.4 1.6 - - - -
157A THR* 3.3 12.3 - - + +
159A ILE* 4.3 14.8 - - + -
215A MET* 4.1 21.5 - - + -
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Residues in contact with GLY 127 (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* 3.5 10.5 - - - -
126A VAL* 1.3 74.4 - - - +
128A VAL* 1.3 63.0 + - - +
151A LEU* 5.0 1.3 - - - -
155A CYS* 3.6 14.6 - - - -
157A THR 2.8 13.1 + - - -
158A LEU* 3.6 19.5 - - - -
159A ILE* 2.8 27.9 + - - +
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Residues in contact with VAL 128 (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 PHE* 3.7 30.5 - - + -
98A VAL 2.9 8.5 + - - -
99A THR* 3.0 36.8 - - + -
100A ALA 3.5 0.2 + - - -
126A VAL* 4.0 6.5 - - + +
127A GLY* 1.3 78.7 - - - +
129A VAL* 1.3 60.9 + - - +
158A LEU* 4.2 0.4 - - - +
159A ILE* 3.6 16.2 - - + +
161A ILE* 4.1 14.6 - - + -
187A LEU* 3.4 34.0 - - + +
190A GLY* 4.7 8.1 - - - -
191A VAL* 3.9 9.2 - - + +
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Residues in contact with VAL 129 (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 4.1 5.2 - - - +
100A ALA* 3.2 27.4 - - + +
102A GLU* 3.8 28.9 - - + +
128A VAL* 1.3 81.9 - - - +
130A THR* 1.3 62.9 + - - +
148A ILE* 4.3 11.4 - - + -
151A LEU* 3.6 22.9 - - + -
158A LEU* 3.8 18.8 - - + -
159A ILE 3.1 6.2 + - - +
160A VAL* 3.5 6.1 - - + -
161A ILE* 2.8 26.5 + - - +
187A LEU* 3.9 2.5 - - - -
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Residues in contact with THR 130 (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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100A ALA 3.4 2.8 + - - -
101A GLY* 3.5 17.8 - - - -
102A GLU* 3.1 29.8 + - - +
129A VAL* 1.3 76.3 - - - +
131A ARG* 1.3 60.6 + - - +
132A PRO 4.1 0.2 - - - -
160A VAL* 5.0 1.6 - - - -
161A ILE* 3.0 16.6 - - + +
163A ASN* 3.4 32.8 + - - +
183A ALA* 4.5 9.4 - - + +
186A VAL* 4.7 0.9 - - + -
187A LEU* 3.7 33.0 - - + +
380A GDP 4.9 6.2 + - - -
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Residues in contact with ARG 131 (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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102A GLU* 4.8 0.4 - - - -
130A THR* 1.3 73.0 - - - +
132A PRO* 1.3 79.9 - - + +
141A SER* 5.7 1.7 + - - +
144A ALA* 4.7 3.1 - - + -
145A GLU* 2.9 44.6 + - - +
148A ILE* 3.8 33.0 - - + +
160A VAL* 3.6 24.2 - - + +
161A ILE 2.8 8.0 + - - +
162A PRO* 3.9 23.1 - - + +
163A ASN* 3.1 23.8 + - - +
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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