Contacts of the strand formed by residues 88 - 97 (chain A) in PDB entry 2DLH
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A MET* 4.3 15.2 - - - +
60A PRO* 5.5 5.0 - - + +
87A LYS* 1.3 73.9 - - - +
89A TYR* 1.3 68.2 + - - +
90A SER* 5.5 0.4 - - - +
109A GLN* 3.8 30.5 - - + +
110A VAL 4.2 4.9 - - - +
111A ILE* 4.0 20.0 - - + +
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Residues in contact with TYR 89 (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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35A ILE* 6.2 2.9 - - + -
56A TYR* 4.9 10.1 - + + -
57A THR* 3.8 12.6 - - - -
58A MET* 2.9 60.1 - - + +
68A MET* 5.4 5.0 - - + +
83A LEU* 4.2 32.2 - - + +
84A VAL* 3.7 33.6 + - + +
87A LYS* 3.3 23.1 + - + -
88A THR* 1.3 73.9 - - - +
90A SER* 1.3 62.6 + - - +
91A VAL* 4.0 2.0 + - + -
109A GLN* 3.3 6.4 - - - +
110A VAL* 3.1 46.4 + - + +
112A THR* 4.2 11.9 - - + -
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Residues in contact with SER 90 (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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55A TYR 4.0 1.6 - - - -
56A TYR* 3.1 23.6 - - - +
57A THR 3.8 8.6 + - - -
60A PRO* 3.0 27.8 - - - +
67A TRP* 3.5 27.1 - - - -
88A THR* 5.5 0.2 - - - +
89A TYR* 1.3 71.6 - - - +
91A VAL* 1.3 71.3 + - - +
92A LYS* 5.6 0.7 - - - -
108A ILE 3.7 0.2 - - - -
109A GLN* 2.7 33.7 + - - -
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Residues in contact with VAL 91 (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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27A ALA* 4.9 5.6 - - + -
35A ILE* 5.0 11.2 - - + -
37A VAL* 4.1 32.5 - - + -
54A VAL* 4.3 12.6 - - + -
55A TYR 3.3 4.0 - - - -
56A TYR* 4.6 6.7 - - + -
80A ILE* 6.0 0.2 - - + -
89A TYR* 4.1 3.8 - - + +
90A SER* 1.3 82.8 - - - +
92A LYS* 1.3 72.9 + - - +
93A VAL* 4.8 1.6 - - + -
106A SER 4.8 0.3 - - - +
107A ASP* 4.3 0.9 - - - -
108A ILE* 3.2 49.2 + - + +
110A VAL* 4.1 25.8 - - + -
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Residues in contact with LYS 92 (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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25A VAL* 6.0 0.9 - - - -
54A VAL* 3.2 6.6 - - - +
55A TYR* 2.9 40.3 + - + -
64A VAL* 3.9 21.0 - - + +
67A TRP* 3.9 29.8 - - + -
90A SER* 5.6 0.2 - - - -
91A VAL* 1.3 82.8 - - - +
93A VAL* 1.3 72.4 + - - +
104A LEU* 4.2 25.7 - - + +
105A SER* 4.3 17.1 + - - +
107A ASP* 4.1 29.9 + - + +
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Residues in contact with VAL 93 (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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22A PRO* 3.1 22.1 - - + +
25A VAL* 3.9 20.2 - - + -
37A VAL* 4.2 7.9 - - + -
39A TRP* 3.5 59.2 - - + +
52A TYR* 4.7 0.2 - - + -
53A ARG 3.5 7.9 - - - +
54A VAL* 4.4 4.0 - - + -
55A TYR* 5.1 0.2 - - - -
91A VAL* 4.8 1.3 - - + -
92A LYS* 1.3 85.2 - - - +
94A LEU* 1.3 71.0 + - - +
104A LEU* 3.7 2.8 - - - -
105A SER* 3.1 30.0 + - - +
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Residues in contact with LEU 94 (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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22A PRO* 3.9 10.3 - - - -
52A TYR* 3.2 29.0 - - - +
53A ARG* 3.3 14.6 + - + -
55A TYR* 3.1 41.3 - - + +
93A VAL* 1.3 78.6 - - - +
95A ALA* 1.3 90.4 + - - +
96A PHE* 4.0 12.3 - - + +
101A ASP* 4.7 5.2 - - + -
102A GLY 3.6 17.7 - - - +
103A PRO 3.9 3.1 - - - +
104A LEU* 3.7 27.4 - - + -
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Residues in contact with ALA 95 (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 PRO* 2.9 16.9 - - + +
20A SER 4.5 5.1 + - - +
22A PRO* 4.6 6.6 - - + +
42A PRO* 4.0 26.9 - - + -
49A ILE* 4.6 3.4 - - + -
52A TYR* 3.7 22.7 - - + -
94A LEU* 1.3 78.1 - - - +
96A PHE* 1.3 54.7 + - - +
102A GLY* 2.7 32.4 + - - -
103A PRO 4.6 3.0 + - - -
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Residues in contact with PHE 96 (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 PRO* 3.5 4.9 - - - -
49A ILE* 4.0 1.9 - - - +
50A GLN* 3.7 26.2 + - + -
51A GLY* 3.5 26.1 + - - +
52A TYR* 3.1 40.8 - - - -
53A ARG* 4.3 13.0 - - + -
72A VAL 5.1 3.4 - - - -
94A LEU* 4.2 7.6 - - + -
95A ALA* 1.3 77.5 - - - +
97A THR* 1.3 75.3 + - - +
100A GLY 3.5 10.8 - - - +
101A ASP* 3.8 12.1 - - + -
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Residues in contact with THR 97 (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 GLN 3.6 4.5 + - - -
17A ALA* 3.5 12.0 - - - -
18A PRO* 3.3 21.0 - - + +
45A PRO 4.1 6.7 - - - +
47A GLY* 4.0 13.2 - - - +
48A GLN 3.8 16.8 - - - +
49A ILE* 3.2 33.4 - - + -
50A GLN* 4.4 4.9 - - - +
96A PHE* 1.3 81.6 - - - +
98A SER* 1.3 65.0 + - - +
99A ILE* 3.6 8.4 + - - +
100A GLY* 2.9 20.5 + - - +
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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