Contacts of the strand formed by residues 124 - 135 (chain A) in PDB entry 4DQ0
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLU* 5.2 1.6 - - - -
96A TYR 3.6 7.4 - - - +
97A ASP 4.8 0.2 - - - +
99A ILE* 3.5 5.5 - - + +
120A MET 2.7 21.1 + - - -
121A GLN 3.2 9.5 + - - -
122A ARG 4.1 2.6 - - - +
123A CYS* 1.3 78.7 - - - +
125A LYS* 1.3 72.8 + - - +
126A PRO* 3.7 1.4 - - - +
128A GLY* 3.7 25.4 - - - +
129A TYR 3.9 2.7 - - - +
130A ASN* 2.9 26.1 + - - +
163A TRP* 3.7 15.0 - - + -
196A LYS* 3.0 25.7 + - + -
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Residues in contact with LYS 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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33A LYS* 5.2 4.4 - - - +
95A GLU* 3.2 50.6 + - + +
96A TYR 2.9 17.0 + - - +
97A ASP* 3.5 35.1 + - - +
123A CYS 4.0 0.6 + - - -
124A THR* 1.3 76.3 - - - +
126A PRO* 1.3 69.1 - - + +
127A GLY 3.3 0.2 + - - -
128A GLY* 2.6 31.5 + - - +
196A LYS* 3.9 2.3 - - - +
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Residues in contact with PRO 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 GLU* 4.8 4.5 - - - +
124A THR 3.7 3.6 - - - +
125A LYS* 1.3 91.8 - - + +
127A GLY* 1.3 59.2 + - - +
128A GLY 3.4 0.2 + - - -
196A LYS* 4.2 15.7 - - + +
197A LYS 3.4 19.3 - - - +
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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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126A PRO* 1.3 71.2 - - - +
128A GLY* 1.3 62.0 + - - +
129A TYR* 3.7 7.3 - - - -
195A ARG* 3.0 38.6 + - - +
196A LYS 2.7 21.3 + - - -
197A LYS 3.7 2.6 + - - -
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Residues in contact with GLY 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 ASP* 3.3 19.7 - - - -
124A THR* 3.7 10.3 - - - -
125A LYS* 2.6 25.8 + - - +
126A PRO 3.1 0.8 + - - -
127A GLY* 1.3 75.1 - - - +
129A TYR* 1.3 58.9 + - - -
195A ARG* 3.3 3.5 - - - -
196A LYS 2.8 27.7 + - - -
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Residues in contact with TYR 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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28A VAL* 4.1 19.6 + - + +
29A VAL* 3.7 34.5 - - + -
30A LYS 5.7 0.4 - - - -
97A ASP 2.8 9.8 + - - -
98A PHE* 3.4 19.0 + - + -
99A ILE 3.0 19.8 + - - -
124A THR* 3.9 1.5 - - - +
127A GLY 3.7 14.8 - - - -
128A GLY* 1.3 76.0 - - - -
130A ASN* 1.3 71.2 + - - +
163A TRP* 4.4 0.2 - - - -
166A VAL* 4.2 13.5 - - + +
193A LEU* 3.8 26.5 - - + -
194A ALA 3.1 15.5 - - - +
195A ARG* 3.5 40.9 + - + -
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Residues in contact with ASN 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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99A ILE* 3.3 14.6 - - - +
120A MET* 3.8 23.9 - - + +
124A THR* 2.9 27.9 + - - +
129A TYR* 1.3 85.0 + - - +
131A LEU* 1.3 60.7 + - - +
132A ILE* 5.1 0.2 - - + -
160A TYR* 2.7 42.9 + - + +
163A TRP* 3.6 14.8 - - + -
192A MET* 3.6 5.5 - - + +
193A LEU* 3.5 5.1 - - - +
194A ALA* 2.9 32.8 + - - +
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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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21A GLU* 4.1 33.0 - - + +
22A VAL* 3.9 20.4 - - + -
25A ALA* 4.4 6.5 - - + -
98A PHE* 3.9 20.2 - - + -
99A ILE 2.9 7.6 + - - +
100A LEU* 3.3 10.8 - - + -
101A SER 3.0 26.9 + - - -
102A THR* 3.8 26.0 - - + -
130A ASN* 1.3 73.7 - - - +
132A ILE* 1.3 70.9 + - - +
133A VAL* 4.6 2.5 - - + -
167A LYS* 6.1 1.1 - - + -
191A THR* 5.3 1.3 - - + -
192A MET 3.3 18.4 - - - +
193A LEU* 4.3 13.0 - - + -
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Residues in contact with ILE 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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101A SER* 3.5 11.7 - - - +
105A LEU* 4.2 25.1 - - + -
117A ILE* 4.7 3.4 - - + -
120A MET* 3.8 23.6 - - + -
130A ASN* 4.1 1.0 - - + -
131A LEU* 1.3 81.2 - - - +
133A VAL* 1.3 74.1 + - - +
134A ALA 4.6 0.2 - - - +
151A PHE* 4.3 5.2 - - + -
156A LEU* 3.8 29.8 - - + -
160A TYR* 3.5 38.6 - - + +
190A ALA 3.7 0.5 - - - +
191A THR* 3.4 3.3 - - - -
192A MET* 2.8 42.6 + - + +
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Residues in contact with VAL 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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19A HIS* 4.1 17.9 - - + +
21A GLU* 3.8 31.2 - - + -
101A SER 3.2 9.9 + - - +
102A THR* 4.2 10.8 - - + -
103A VAL* 2.8 48.5 + - + +
104A VAL 4.2 1.2 + - - -
105A LEU* 5.2 0.7 + - - +
131A LEU* 4.6 2.2 - - + -
132A ILE* 1.3 79.9 - - - +
134A ALA* 1.3 65.8 + - - +
189A PHE* 4.7 11.4 - - + -
190A ALA 3.3 4.7 - - - +
191A THR* 4.0 19.3 - - + +
178B THR* 5.8 0.4 - - - +
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Residues in contact with ALA 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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105A LEU* 4.3 15.3 - - + -
106A MET* 3.9 16.8 - - + +
132A ILE* 4.3 2.2 - - + +
133A VAL* 1.3 77.3 - - - +
135A ALA* 1.3 63.4 + - - +
149A PHE* 5.8 1.1 - - + -
151A PHE* 3.6 32.1 - - + -
189A PHE* 3.4 6.6 - - - -
190A ALA* 2.7 40.4 + - - +
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Residues in contact with ALA 135 (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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106A MET* 3.6 23.6 - - + +
134A ALA* 1.3 79.6 - - - +
136A MET* 1.3 62.7 + - - +
147A PHE* 3.5 38.1 - - + -
149A PHE 5.0 0.2 - - - +
150A ALA* 3.6 6.5 - - + -
151A PHE* 3.1 20.3 + - - +
187A LEU* 4.4 6.1 - - + -
188A ARG 3.8 0.2 - - - -
189A PHE* 3.7 17.5 - - + -
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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