Contacts of the strand formed by residues 186 - 198 (chain A) in PDB entry 1F5J
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.2 4.7 - - - +
38A TRP* 3.0 46.4 + - - +
71A ASN 3.6 7.4 - - - -
73A ASN* 3.4 15.8 - - - +
185A SER* 1.3 77.6 + - - +
187A SER* 1.3 61.2 + - - -
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Residues in contact with SER 187 (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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36A CYS 3.3 6.7 - - - -
37A GLN* 3.5 23.8 - - - -
38A TRP* 3.7 6.6 - - - -
71A ASN* 2.8 47.9 + - - +
72A PRO 4.1 0.2 - - - -
186A GLY* 1.3 76.3 - - - -
188A ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 188 (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 SER* 3.4 3.3 - - - -
36A CYS* 2.9 40.3 + - - +
38A TRP* 4.7 0.2 - - + -
69A THR* 3.1 14.1 - - - +
70A TYR* 4.2 11.9 - - + -
179A VAL* 3.9 31.2 - - + -
187A SER* 1.3 79.2 - - - +
189A ASN* 1.3 62.3 + - - +
190A ILE* 4.2 4.9 - - + -
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Residues in contact with ASN 189 (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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29A TYR* 4.4 9.3 - - - -
34A PHE 3.5 8.4 + - - -
35A SER* 3.4 24.3 - - - -
68A ALA* 3.5 0.2 - - - -
69A THR* 2.7 46.3 + - + -
188A ALA* 1.3 76.8 - - - +
190A ILE* 1.3 69.3 + - - +
191A THR* 3.4 21.8 + - - +
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Residues in contact with ILE 190 (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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32A GLY 4.0 19.1 - - - +
33A ARG* 3.2 8.4 - - - +
34A PHE* 2.8 65.0 + - + +
67A SER 3.7 3.8 - - - +
68A ALA* 4.0 16.8 - - + -
78A LEU* 4.5 2.5 - - + -
177A LEU* 3.5 34.5 - - + -
179A VAL* 3.7 21.5 - - + -
188A ALA* 4.4 2.5 - - + -
189A ASN* 1.3 81.6 + - - +
191A THR* 1.3 59.9 + - - +
192A GLN 3.7 13.7 - - - +
193A ASN* 4.2 0.2 - - + -
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Residues in contact with THR 191 (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 ARG* 3.2 26.8 + - - +
67A SER* 3.0 28.8 + - - -
68A ALA* 4.4 1.4 - - - -
69A THR* 4.6 7.1 + - - +
189A ASN* 3.4 30.0 + - - +
190A ILE* 1.3 72.3 - - - +
192A GLN* 1.3 62.2 + - - +
9B THR* 3.5 38.5 - - + +
11B ASP* 4.6 3.3 + - - -
12B GLY 3.7 8.3 + - - -
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Residues in contact with GLN 192 (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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31A GLN 5.2 0.4 - - - -
33A ARG* 4.0 4.9 - - - +
65A THR* 3.4 37.2 - - - +
66A TYR* 3.1 9.8 - - - +
67A SER* 3.1 45.3 + - - +
190A ILE* 3.5 6.5 - - - +
191A THR* 1.3 81.6 - - - +
193A ASN* 1.3 66.5 + - - +
194A THR* 3.8 17.2 + - - +
11B ASP* 3.8 32.5 + - - +
12B GLY* 3.8 6.0 - - - +
13B TYR* 5.8 0.7 - - - -
50B LYS* 4.4 5.7 + - - -
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Residues in contact with ASN 193 (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 TYR* 2.5 40.2 + - - -
31A GLN 3.8 9.3 + - - +
32A GLY 3.9 14.1 - - - +
48A THR* 3.1 40.8 + - - -
64A ILE* 3.4 15.4 - - - +
65A THR 3.7 3.6 - - - -
66A TYR* 4.4 0.9 - - - +
177A LEU* 3.5 23.8 - - + +
190A ILE* 4.2 0.4 - - + -
192A GLN* 1.3 76.4 - - - +
194A THR* 1.3 56.2 + - - +
195A PHE* 3.4 17.2 - - - -
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Residues in contact with THR 194 (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 TYR* 3.9 5.2 - - - +
63A ARG 3.6 1.0 - - - +
64A ILE* 3.2 6.1 - - - -
65A THR* 2.9 48.8 + - - -
192A GLN* 3.8 19.1 + - - +
193A ASN* 1.3 73.3 + - - +
195A PHE* 1.3 74.1 + - - +
196A SER* 5.5 2.4 - - - -
11B ASP* 5.5 1.0 + - - -
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Residues in contact with PHE 195 (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 TYR* 4.1 11.6 + + - -
49A GLY* 3.8 13.5 - - - -
50A LYS* 3.6 22.9 - - + -
52A TYR* 3.2 27.1 - - - +
62A ILE* 4.6 5.2 - - + -
63A ARG 3.6 2.9 - - - -
64A ILE* 3.5 31.2 - - + -
175A ILE* 3.4 29.2 - - + -
176A THR* 4.5 2.2 - - - -
193A ASN* 3.4 36.3 + - - -
194A THR* 1.3 88.2 - - - +
196A SER* 1.3 62.6 - - - +
197A GLN* 6.4 0.7 - - + -
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Residues in contact with SER 196 (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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61A THR 3.5 1.4 - - - +
62A ILE* 3.3 5.5 - - - +
63A ARG* 2.8 54.6 + - - +
65A THR* 5.7 0.5 + - - -
194A THR* 5.5 2.7 - - - -
195A PHE* 1.3 76.9 - - - +
197A GLN* 1.3 60.0 + - - +
198A SER* 4.3 0.4 - - - -
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Residues in contact with GLN 197 (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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52A TYR* 4.0 15.7 - - + +
54A GLN* 4.9 5.5 + - - +
59A LEU* 3.1 49.2 + - - +
61A THR 3.2 4.0 - - - +
62A ILE* 4.1 16.3 - - + +
195A PHE* 4.3 0.9 - - + -
196A SER* 1.3 74.5 - - - +
198A SER* 1.3 65.0 + - - +
199A SER* 6.0 0.4 - - - +
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Residues in contact with SER 198 (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 LEU 4.0 1.4 - - - +
60A GLY* 3.5 2.3 - - - -
61A THR* 2.5 50.4 + - - +
196A SER 4.3 0.6 - - - -
197A GLN* 1.3 76.1 - - - +
199A SER* 1.3 64.9 + - - +
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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