Contacts of the strand formed by residues 108 - 123 (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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY 6.0 0.7 - - - -
102A HIS* 3.4 2.6 + - - +
103A SER* 3.2 6.9 - - - -
104A GLY 2.9 39.9 + - - -
105A ARG 4.7 0.2 - - - -
106A THR 3.5 2.4 + - - -
107A THR* 1.3 80.3 + - - +
109A TYR* 1.3 59.4 + - - -
110A GLN 3.9 0.5 + - - -
202A GOL 3.9 13.0 - - - -
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Residues in contact with TYR 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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79A VAL* 4.5 4.0 - - + -
80A ALA 3.5 20.9 - - - +
81A ASN* 3.5 42.0 - - - +
82A GLY 4.6 1.5 - - - +
86A VAL* 3.5 28.6 - - + +
101A CYS* 3.4 37.9 - - + +
102A HIS 3.3 13.2 - - - -
103A SER* 4.1 3.1 - - - -
107A THR 3.5 0.6 + - - -
108A GLY* 1.3 70.6 - - - -
110A GLN* 1.3 59.9 + - - +
111A CYS* 3.7 9.0 + - - -
148A ILE* 4.1 17.7 + - + +
149A THR 4.9 2.4 + - - -
150A SER* 4.9 5.4 - - - -
202A GOL 2.8 39.5 + - - +
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Residues in contact with GLN 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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101A CYS* 3.1 1.7 - - - -
102A HIS* 2.8 44.0 + - + +
107A THR* 2.9 46.8 + - - +
109A TYR* 1.3 76.1 - - - +
111A CYS* 1.3 63.8 + - - +
136A ALA* 4.0 1.8 - - - +
137A CYS* 3.4 46.7 + - - +
170A CYS* 4.7 1.8 - - - -
202A GOL 3.4 18.5 + - - -
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Residues in contact with CYS 111 (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 3.3 4.3 - - - +
101A CYS* 2.0 46.4 - - - -
109A TYR* 3.7 16.8 - - - -
110A GLN* 1.3 78.3 + - - +
112A GLY* 1.3 59.4 + - - +
135A ASN 5.0 0.2 - - - +
136A ALA* 3.4 15.6 - - - +
137A CYS 4.8 0.7 + - - -
177A ARG* 5.4 2.4 + - - -
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Residues in contact with GLY 112 (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 ALA* 3.3 8.5 - - - +
100A VAL 2.8 27.5 + - - +
111A CYS* 1.3 78.4 - - - +
113A THR* 1.3 66.6 + - - +
134A SER* 4.4 1.1 - - - -
135A ASN* 3.4 11.7 - - - -
136A ALA* 3.6 7.9 - - - +
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Residues in contact with THR 113 (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 GLY* 4.2 13.5 - - - +
98A ALA 3.2 12.8 - - - +
99A ALA* 4.1 9.2 - - + +
100A VAL* 4.2 1.6 - - - +
112A GLY* 1.3 79.7 - - - +
114A ILE* 1.3 66.0 + - - +
115A THR* 3.6 7.8 + - - +
134A SER* 2.8 27.1 + - - -
135A ASN* 2.8 28.9 + - - +
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Residues in contact with ILE 114 (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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94A ALA* 3.9 34.1 - - + +
95A ALA 3.9 11.7 - - - +
96A VAL* 3.7 19.7 - - + +
97A GLY* 2.8 26.9 + - - -
98A ALA* 2.9 18.0 + - + +
100A VAL* 3.9 23.6 - - + -
113A THR* 1.3 73.1 + - - +
115A THR* 1.3 60.5 + - - +
116A ALA 4.1 6.3 - - - +
117A LYS* 4.6 3.1 - - - -
132A THR* 3.6 27.6 - - + -
133A GLN 3.5 4.9 - - - +
134A SER* 4.3 0.7 - - - +
155A GLN* 4.6 4.0 - - - +
181A PHE* 4.6 16.2 - - + -
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Residues in contact with THR 115 (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* 3.8 14.1 - - - +
113A THR* 3.9 19.5 - - - +
114A ILE* 1.3 75.8 - - - +
116A ALA* 1.3 59.2 + - - +
133A GLN* 2.8 46.3 + - - +
134A SER* 3.8 1.7 + - - -
135A ASN* 4.1 21.5 - - + +
177A ARG 5.4 0.7 + - - -
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Residues in contact with ALA 116 (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* 4.1 8.3 - - - -
114A ILE* 3.8 2.5 - - - +
115A THR* 1.3 84.2 + - - +
117A LYS* 1.3 66.7 + - - +
119A VAL* 4.1 13.7 - - + -
132A THR* 3.5 8.3 - - - +
133A GLN* 2.8 42.7 + - - +
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Residues in contact with LYS 117 (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* 3.0 29.1 + - - +
94A ALA 2.8 30.2 + - - -
95A ALA* 3.9 5.2 - - - +
96A VAL* 4.0 26.2 - - + +
114A ILE* 4.6 6.1 - - - -
116A ALA* 1.3 81.0 - - - +
118A ASN* 1.3 73.7 + - + +
119A VAL* 3.3 7.2 + - - +
131A LEU 3.9 4.0 - - - -
132A THR* 3.8 19.5 - - + +
183A ARG* 5.9 2.2 - - - -
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Residues in contact with ASN 118 (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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117A LYS* 1.3 79.8 - - + +
119A VAL* 1.3 61.6 + - - +
120A THR* 4.0 3.3 + - - -
129A ARG* 5.3 2.0 - - - +
130A GLY* 3.3 31.0 + - - +
131A LEU 3.1 8.1 + - - -
132A THR* 5.0 0.2 + - - -
183A ARG* 6.3 0.4 - - - +
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Residues in contact with VAL 119 (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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116A ALA* 4.1 21.1 - - + -
117A LYS 3.9 11.7 - - - +
118A ASN* 1.3 73.5 - - - +
120A THR* 1.3 74.8 + - - +
130A GLY 3.5 3.8 + - - -
131A LEU* 2.8 47.0 + - - +
133A GLN* 4.1 19.5 - - + +
178A SER* 5.5 0.7 - - - +
180A LEU* 4.0 24.0 - - + -
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Residues in contact with THR 120 (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 4.0 3.4 + - - -
119A VAL* 1.3 85.3 - - - +
121A ALA* 1.3 70.1 + - - +
122A ASN* 3.9 21.6 + - - +
127A ALA* 4.0 13.0 - - + -
128A VAL 3.3 11.2 - - - +
129A ARG* 3.9 27.6 + - + +
180A LEU* 5.2 0.5 - - - +
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Residues in contact with ALA 121 (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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119A VAL 4.0 0.8 + - - -
120A THR* 1.3 72.8 - - - +
122A ASN* 1.3 62.6 + - - +
123A TYR* 3.5 37.5 + - + -
127A ALA* 3.3 4.5 - - - +
128A VAL* 2.8 32.3 + - - +
131A LEU* 3.7 16.8 - - + -
180A LEU* 3.7 13.9 - - + -
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Residues in contact with ASN 122 (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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120A THR* 3.9 20.2 + - - +
121A ALA* 1.3 72.1 - - - +
123A TYR* 1.3 67.8 + - - +
126A GLY 4.4 2.9 - - - -
127A ALA* 4.0 10.4 - - - +
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Residues in contact with TYR 123 (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 13.9 - + + -
121A ALA* 3.5 26.0 + - + +
122A ASN* 1.3 78.6 - - - +
124A ALA* 1.3 67.5 + - - +
125A GLU* 3.7 12.8 - - - +
126A GLY* 3.1 23.8 + - - +
128A VAL* 3.5 33.4 - - + -
131A LEU* 3.9 3.1 - - - +
159A SER* 2.8 29.8 + - - -
160A GLY* 3.2 21.6 + - - -
161A GLY 5.0 3.1 - - - -
180A LEU* 4.4 2.1 - - + +
201A GOL 3.7 34.5 - - - -
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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