Contacts of the strand formed by residues 39 - 49 (chain A) in PDB entry 6I53
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.1 24.0 + - - +
32A PRO* 3.2 20.8 + - + +
38A VAL* 1.3 71.0 - - - +
40A GLU* 1.3 58.3 + - - +
41A VAL* 3.1 17.2 + - + -
70A TRP* 4.3 15.3 - - + -
71A LYS 5.2 4.0 - - - +
95A TRP* 4.0 27.4 - - + -
166A GLU 2.9 13.1 + - - -
167A VAL* 3.6 13.2 - - - +
168A VAL 3.2 18.9 + - - -
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Residues in contact with GLU 40 (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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38A VAL* 3.8 10.6 + - + +
39A THR* 1.3 67.3 - - - +
41A VAL* 1.3 61.0 + - - +
42A LYS* 3.6 36.3 + - + +
69A SER 3.7 6.1 - - - +
70A TRP* 3.8 10.8 - - - +
71A LYS 4.8 1.6 + - - -
168A VAL* 3.4 17.0 - - + +
170A GLU* 2.9 30.4 - - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 3.1 24.2 + - + +
40A GLU* 1.3 72.5 - - - +
42A LYS* 1.3 61.7 + - - +
43A THR* 3.9 8.5 + - + -
68A GLN* 4.4 13.0 - - + -
69A SER 3.4 7.6 - - - +
70A TRP* 4.1 8.7 - - + -
95A TRP* 4.8 1.1 - - + -
97A PRO* 4.3 25.8 - - + -
167A VAL* 3.8 15.5 - - + -
168A VAL 3.0 7.4 + - - +
169A TYR* 3.4 31.5 - - + -
170A GLU* 3.1 25.6 + - - +
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Residues in contact with LYS 42 (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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40A GLU* 3.6 35.4 - - + +
41A VAL* 1.3 76.0 - - - +
43A THR* 1.3 61.3 + - - +
68A GLN 3.3 3.1 - - - -
69A SER* 2.5 55.7 + - - +
170A GLU* 3.3 11.2 - - + +
171A TRP 5.5 0.9 - - - +
172A THR* 3.7 25.7 - - + +
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Residues in contact with THR 43 (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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41A VAL* 4.3 6.1 - - + +
42A LYS* 1.3 77.2 - - - +
44A ASP* 1.3 66.1 + - - +
66A PHE* 4.7 2.0 - - + -
67A ARG 3.4 12.6 - - - +
68A GLN* 4.4 5.6 - - + -
157A PHE* 3.8 24.7 - - + -
169A TYR* 3.6 33.9 - - + -
170A GLU 3.3 10.3 + - - -
171A TRP* 3.4 26.4 - - - -
172A THR* 3.4 24.4 + - - +
178A SER* 5.0 0.2 - - - -
213A MET* 4.3 2.8 - - - +
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Residues in contact with ASP 44 (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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43A THR* 1.3 79.2 + - - +
45A ILE* 1.3 79.0 + - - +
46A PHE 4.4 0.2 - - - -
66A PHE* 3.9 0.7 - - - -
67A ARG* 2.7 67.9 + - + +
171A TRP* 4.3 2.4 - - - -
172A THR* 4.2 6.7 - - + +
173A ARG* 2.5 42.5 + - - +
178A SER 2.9 20.3 - - - +
180A VAL* 5.3 1.2 - - - +
201B ALA* 5.2 0.9 - - - +
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Residues in contact with ILE 45 (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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44A ASP* 1.3 91.4 + - - +
46A PHE* 1.3 60.6 + - - +
47A VAL* 3.8 15.5 - - + -
64A VAL* 3.7 29.4 - - + -
65A PHE 3.7 2.7 - - - -
66A PHE* 3.7 19.5 - - + -
67A ARG* 4.4 0.2 - - - -
101A PHE* 5.6 0.9 - - + -
155A LEU* 4.5 16.8 - - + -
157A PHE* 3.6 30.5 - - + -
171A TRP* 3.8 14.4 - - + -
178A SER 3.4 3.4 + - - -
179A VAL* 3.5 18.8 - - + -
180A VAL* 3.3 24.1 + - - +
215A THR* 4.6 3.4 - - - +
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Residues in contact with PHE 46 (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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45A ILE* 1.3 72.1 - - - +
47A VAL* 1.3 61.0 + - - +
48A THR* 3.3 17.4 + - + +
65A PHE* 2.9 52.8 + + + -
67A ARG* 3.4 29.6 - - - +
180A VAL* 3.6 25.6 - - + -
181A VAL 5.0 0.4 - - - -
182A ALA* 3.7 34.1 - - + -
200B PHE* 3.5 31.0 - + - -
201B ALA* 6.3 0.7 - - + -
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Residues in contact with VAL 47 (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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45A ILE* 3.8 20.9 - - + -
46A PHE* 1.3 69.7 - - - +
48A THR* 1.3 61.8 + - - +
49A SER 4.0 9.0 - - - +
50A PHE* 4.1 17.0 - - + +
62A ILE* 3.8 38.6 - - + -
63A ASP 3.8 3.6 - - - +
64A VAL* 3.9 1.6 - - + -
179A VAL* 4.2 3.8 - - + -
180A VAL 2.9 16.6 + - - +
181A VAL* 4.1 15.6 - - + +
182A ALA* 2.7 30.1 + - - +
217A PHE* 3.8 17.3 - - + -
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Residues in contact with THR 48 (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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46A PHE* 3.7 13.9 - - + +
47A VAL* 1.3 73.5 - - - +
49A SER* 1.3 62.0 + - - -
63A ASP* 2.7 46.2 + - - +
64A VAL 4.7 0.9 - - - -
65A PHE* 3.6 40.4 - - + +
132A ARG* 6.2 0.9 - - + -
181A VAL* 5.8 0.2 - - - -
182A ALA* 3.6 15.6 - - - +
185A GLY* 3.3 22.2 + - - +
99B LEU* 4.6 16.9 + - + +
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Residues in contact with SER 49 (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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47A VAL* 3.5 4.1 - - - -
48A THR* 1.3 86.2 + - - +
50A PHE* 1.3 61.5 + - - +
51A GLY* 3.2 4.9 + - - -
62A ILE* 3.8 0.2 - - - -
63A ASP* 3.1 31.4 + - - +
185A GLY* 3.7 15.9 - - - -
187A ARG* 3.1 49.7 + - - -
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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