Contacts of the strand formed by residues 126 - 134 (chain A) in PDB entry 1QRW
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 GLY 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 4.1 10.5 - - - +
122A ASN* 4.9 0.9 - - - -
123A TYR* 3.1 35.1 + - - +
124A ALA 3.3 1.0 + - - -
125A GLU* 1.3 80.5 - - - +
127A ALA* 1.3 65.3 + - - -
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Residues in contact with ALA 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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60A PRO* 3.5 1.6 - - - +
61A GLY* 2.8 25.5 + - - -
120A THR* 4.0 6.1 - - + -
121A ALA 3.3 10.5 - - - +
122A ASN* 4.0 15.0 - - - +
126A GLY* 1.3 74.2 - - - -
128A VAL* 1.3 60.5 + - - +
129A ARG* 3.9 34.3 + - - +
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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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59A PHE* 3.8 11.9 - - + -
60A PRO* 4.0 2.2 - - + -
61A GLY 3.4 8.1 - - - +
62A ASN* 3.6 35.9 - - - +
63A ASP* 4.1 5.2 - - + -
119A VAL 3.9 1.6 - - - +
120A THR* 3.3 2.0 - - - -
121A ALA 2.8 32.8 + - - +
123A TYR* 3.5 33.9 - - + -
127A ALA* 1.3 76.4 - - - +
129A ARG* 1.3 65.1 + - - +
131A LEU* 3.8 31.0 - - + +
182A GLU* 5.0 0.2 - - - +
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Residues in contact with ARG 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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61A GLY* 3.0 20.4 + - - +
62A ASN* 4.9 4.3 - - - +
118A ASN* 5.3 2.2 - - - +
119A VAL 4.0 0.7 - - - -
120A THR* 3.9 25.6 + - + +
127A ALA* 3.9 27.7 + - - +
128A VAL* 1.3 84.4 - - - +
130A GLY* 1.3 66.4 + - - +
131A LEU* 3.3 6.1 + - - +
182A GLU* 4.5 4.9 - - - +
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Residues in contact with GLY 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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118A ASN* 3.3 33.8 + - - +
119A VAL 3.5 5.3 + - - -
120A THR* 4.8 0.2 + - - -
129A ARG* 1.3 76.4 - - - +
131A LEU* 1.3 63.3 + - - +
132A THR 3.9 0.5 + - - -
181A PHE 4.9 0.2 - - - +
182A GLU* 4.8 4.2 - - - +
183A ARG* 4.1 22.0 + - - +
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Residues in contact with LEU 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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63A ASP* 5.1 0.2 - - + -
117A LYS 3.7 0.7 - - - -
118A ASN 3.1 5.8 + - - -
119A VAL* 2.8 43.8 + - - +
121A ALA* 3.7 30.7 - - + -
123A TYR* 3.9 9.4 - - - +
128A VAL* 3.8 30.7 - - + +
129A ARG 4.1 1.3 - - - +
130A GLY* 1.3 77.1 - - - +
132A THR* 1.3 60.7 + - - +
159A SER* 4.0 9.0 - - - +
180A LEU* 3.9 24.0 - - + -
181A PHE 3.6 18.6 - - - +
182A GLU* 3.7 28.0 - - + +
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Residues in contact with THR 132 (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 GLU* 4.9 0.7 + - - -
114A ILE* 3.6 22.2 - - + -
116A ALA 3.5 13.0 - - - +
117A LYS* 3.8 21.7 - - + +
118A ASN 5.0 0.2 + - - -
130A GLY 3.9 0.4 + - - -
131A LEU* 1.3 73.0 - - - +
133A GLN* 1.3 61.3 + - - +
179A SER 3.7 0.9 - - - +
180A LEU* 3.3 4.9 - - - -
181A PHE* 2.9 71.7 + - + -
183A ARG* 3.7 22.3 - - - +
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Residues in contact with GLN 133 (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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114A ILE* 3.5 8.3 - - - +
115A THR* 2.8 43.3 + - - +
116A ALA* 2.8 32.5 + - - +
119A VAL* 4.1 16.4 - - + +
131A LEU 4.0 0.6 + - - -
132A THR* 1.3 75.0 - - - +
134A SER* 1.3 70.2 + - - +
177A ARG 4.8 4.0 + - - +
178A SER* 2.9 29.4 + - - +
179A SER 3.4 3.8 - - - +
180A LEU* 3.6 17.7 - - + +
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Residues in contact with SER 134 (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 VAL* 3.7 6.3 - - - +
113A THR 2.8 25.9 + - - -
114A ILE* 4.4 0.7 - - - -
115A THR* 3.9 6.1 - - - -
133A GLN* 1.3 76.9 - - - +
135A ASN* 1.3 59.3 + - - +
136A ALA* 3.1 14.9 + - - +
147A TRP* 3.4 36.5 - - - -
177A ARG 3.9 5.8 - - - +
179A SER* 2.8 31.0 + - - -
181A PHE* 4.9 3.6 - - - -
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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