Contacts of the strand formed by residues 120 - 131 (chain A) in PDB entry 2DMH
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 ASP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A SER* 5.3 9.6 - - - +
113A LEU 3.8 6.7 - - - -
114A LEU* 3.9 12.8 - - + +
115A ASN* 5.0 0.3 + - - -
118A GLY 4.1 0.4 + - - -
119A GLN* 1.3 80.2 - - - +
121A THR* 1.3 63.8 + - - +
122A GLY* 3.1 6.8 + - - +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASN 4.8 0.2 - - - +
20A PRO* 4.6 20.1 - - - +
88A ILE 3.0 27.8 + - - +
113A LEU* 2.6 32.7 + - - +
114A LEU 3.6 1.1 - - - -
115A ASN* 3.2 42.2 - - + +
119A GLN 2.8 5.2 + - - -
120A ASP* 1.3 73.4 - - - +
122A GLY* 1.3 60.4 + - - +
123A ALA* 3.4 14.3 + - - +
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Residues in contact with GLY 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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18A ASN* 2.9 27.8 - - - +
112A SER* 6.3 0.4 - - - -
113A LEU 4.1 1.4 + - - +
120A ASP* 3.1 10.1 - - - +
121A THR* 1.3 79.9 + - - +
123A ALA* 1.3 59.0 + - - +
124A THR* 4.8 3.4 - - - +
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Residues in contact with ALA 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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17A SER 3.9 1.8 - - - +
18A ASN 3.0 19.7 - - - +
19A ILE* 4.0 13.7 - - + -
20A PRO* 4.1 6.7 - - + -
88A ILE* 5.2 2.2 - - + -
111A ILE 3.3 2.1 - - - +
112A SER* 3.8 1.9 - - - -
113A LEU* 3.1 47.9 + - + +
121A THR* 3.3 9.9 + - - +
122A GLY* 1.3 81.4 - - - +
124A THR* 1.3 63.9 + - - +
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Residues in contact with THR 124 (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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16A ALA* 3.5 3.0 - - - +
17A SER* 2.9 37.6 + - - +
18A ASN* 3.0 26.2 + - - +
110A LEU* 4.4 24.7 - - + +
111A ILE 3.3 11.2 - - - +
112A SER* 5.2 4.9 - - - +
113A LEU* 4.8 1.3 - - - -
122A GLY 4.8 3.8 - - - +
123A ALA* 1.3 80.9 - - - +
125A ILE* 1.3 61.5 + - - +
126A ASP* 5.3 3.4 + - - -
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Residues in contact with ILE 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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13A VAL* 4.6 0.7 - - + -
15A SER 3.6 13.2 - - - +
16A ALA* 4.1 7.2 - - + -
31A VAL* 3.8 33.7 - - + -
53A TRP* 3.9 12.3 - - + -
74A ILE* 4.8 3.8 - - + -
76A VAL* 4.5 9.9 - - + -
91A ALA* 5.7 0.2 - - + -
108A TYR 4.0 0.3 - - - +
110A LEU 4.2 0.2 + - - -
111A ILE* 3.6 36.4 + - + +
113A LEU* 4.1 27.8 - - + -
124A THR* 1.3 75.7 - - - +
126A ASP* 1.3 76.8 + - - +
127A LEU* 4.2 24.9 - - + -
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Residues in contact with ASP 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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13A VAL* 4.7 0.2 - - - +
14A GLU* 3.5 34.4 + - + +
15A SER* 3.2 20.9 + - - +
108A TYR 3.7 4.0 - - - -
109A LYS* 3.5 36.1 - - + +
110A LEU* 3.7 6.8 + - - +
124A THR* 5.3 2.9 + - - -
125A ILE* 1.3 78.2 + - - +
127A LEU* 1.3 76.7 + - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.8 7.6 - - + -
12A ILE 3.4 15.9 - - - +
13A VAL* 3.6 29.8 - - + -
14A GLU* 5.1 0.9 - - - +
31A VAL* 4.9 3.1 - - + -
72A LEU* 5.9 0.7 - - + -
74A ILE* 3.7 40.2 - - + -
93A VAL* 5.1 2.9 - - + -
108A TYR* 2.7 53.8 + - + +
109A LYS* 4.8 0.4 - - - +
111A ILE* 4.3 18.4 - - + -
125A ILE* 4.2 14.6 - - + -
126A ASP* 1.3 89.0 - - - +
128A VAL* 1.3 60.8 + - - +
129A ILE* 4.0 10.1 - - + -
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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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10A ARG 3.5 3.1 - - - +
12A ILE* 3.1 56.3 + - + +
14A GLU* 5.1 12.8 - - + -
105A SER* 4.9 11.0 - - - +
106A LEU 4.3 4.0 - - - +
107A PRO* 4.2 25.6 - - + -
109A LYS* 4.9 10.1 - - - -
127A LEU* 1.3 77.9 - - - +
129A ILE* 1.3 67.6 + - - +
130A GLY 3.9 0.3 + - - -
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Residues in contact with ILE 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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9A LEU* 3.6 30.5 - - + -
10A ARG 3.3 8.7 - - - +
11A VAL* 4.1 12.1 - - + -
72A LEU* 3.8 21.5 - - + -
93A VAL* 3.2 44.2 - - + -
95A LEU* 3.8 14.4 - - + -
98A LEU* 3.8 11.1 - - + +
105A SER* 3.4 3.3 - - - -
106A LEU 3.4 28.3 + - - +
108A TYR* 3.7 13.2 - - + -
127A LEU* 4.0 5.6 - - + -
128A VAL* 1.3 77.1 - - - +
130A GLY* 1.3 61.7 + - - +
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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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8A MET 3.8 1.7 - - - +
9A LEU* 3.6 9.1 - - - -
10A ARG* 2.9 39.0 + - - +
103A SER* 5.9 0.2 - - - -
104A ARG 3.8 5.2 - - - -
105A SER* 3.8 13.9 - - - -
128A VAL* 3.9 1.2 + - - +
129A ILE* 1.3 75.1 - - - +
131A TYR* 1.3 61.8 + - - -
132A ASP* 5.3 0.2 - - - +
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Residues in contact with TYR 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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8A MET 4.4 0.4 - - - -
9A LEU* 4.2 7.0 - - + -
61A LEU* 4.5 8.7 - - + -
65A PRO* 3.7 24.5 - - + +
66A LEU* 3.1 49.3 + - + -
98A LEU* 3.1 36.9 - - + +
99A THR* 4.3 1.3 - - - -
100A GLY 3.3 34.0 + - - -
102A GLN 4.7 6.7 - - - -
103A SER* 3.0 29.3 + - - -
104A ARG 3.1 11.9 + - - +
130A GLY* 1.3 74.0 - - - -
132A ASP* 1.3 85.0 + - - +
133A PRO* 3.4 28.2 - - + +
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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