Contacts of the strand formed by residues 61 - 72 (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 THR 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU 3.5 0.2 + - - -
60A GLY* 1.3 75.0 + - - -
62A ILE* 1.3 63.2 + - - +
63A ARG* 3.9 35.4 - - + +
154A THR* 4.1 8.3 - - + -
156A THR* 3.5 8.2 + - - +
157A ASP* 5.7 0.4 - - - +
196A SER 3.5 1.7 - - - +
197A GLN* 3.2 4.9 - - - -
198A SER* 2.5 48.7 + - - +
199A SER 5.2 4.7 + - - -
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Residues in contact with ILE 62 (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* 3.6 40.8 - - + +
59A LEU* 3.8 32.8 - - + +
61A THR* 1.3 76.1 - - - +
63A ARG* 1.3 68.2 + - - +
64A ILE* 4.7 0.4 - - + -
154A THR* 3.5 4.0 - - - -
155A VAL* 3.0 40.4 + - + -
156A THR* 3.1 21.0 + - + +
175A ILE* 3.9 11.9 - - + -
195A PHE* 4.6 9.6 - - + -
196A SER 3.3 7.0 - - - +
197A GLN* 4.1 16.8 - - + +
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Residues in contact with ARG 63 (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* 3.9 20.6 - - + +
62A ILE* 1.3 78.2 - - - +
64A ILE* 1.3 63.5 + - - +
65A THR* 4.1 1.6 - - - +
152A THR* 4.0 18.6 - - + -
153A VAL 3.4 2.9 - - - -
154A THR* 3.7 30.2 + - + +
194A THR 3.6 1.2 - - - +
195A PHE* 3.6 3.1 - - - -
196A SER* 2.8 48.2 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.7 2.0 - - + -
63A ARG* 1.3 78.5 - - - +
65A THR* 1.3 68.2 + - - +
66A TYR* 3.8 8.4 + - + -
80A ILE* 4.0 28.3 - - + -
151A GLY 3.8 0.7 - - - +
152A THR* 3.3 1.9 - - - -
153A VAL* 2.8 40.8 + - + +
155A VAL* 3.8 15.0 - - + -
175A ILE* 3.7 20.9 - - + -
176A THR 4.9 2.5 - - - +
177A LEU* 5.3 0.2 - - + -
193A ASN* 3.4 22.9 - - - +
194A THR 3.2 6.1 - - - +
195A PHE* 3.5 40.2 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 4.1 2.1 + - - +
64A ILE* 1.3 71.5 + - - +
66A TYR* 1.3 60.8 + - - +
151A GLY* 3.3 12.3 - - - +
152A THR* 3.0 23.1 + - - +
192A GLN* 3.4 30.6 - - - +
194A THR* 2.9 41.8 + - - -
196A SER* 5.7 0.3 + - - -
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.1 17.7 - - + -
65A THR* 1.3 76.5 - - - +
67A SER* 1.3 67.2 + - - +
68A ALA* 4.6 1.3 - - + -
78A LEU* 4.2 14.4 - - + -
80A ILE* 5.2 1.3 - - + -
95A GLU* 2.6 44.8 + - + +
148A ARG* 3.6 9.2 + - - -
149A THR* 3.4 25.1 - - - -
150A SER* 3.2 16.8 + - - -
151A GLY 2.9 50.6 + - - +
153A VAL* 3.9 13.0 - - + -
177A LEU* 3.6 32.5 - - + -
192A GLN* 3.1 19.1 - - - +
193A ASN* 4.5 0.2 - - - -
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Residues in contact with SER 67 (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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66A TYR* 1.3 78.5 - - - +
68A ALA* 1.3 65.3 + - - +
149A THR 3.7 6.3 - - - -
150A SER* 3.7 13.1 + - - -
190A ILE* 3.7 1.9 - - - +
191A THR* 3.0 35.3 + - - -
192A GLN* 3.1 16.8 + - - +
9B THR* 5.2 0.2 - - - +
12B GLY* 2.7 35.6 + - - -
50B LYS* 3.7 2.9 + - - +
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Residues in contact with ALA 68 (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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66A TYR* 4.8 3.1 - - + -
67A SER* 1.3 79.8 + - - +
69A THR* 1.3 64.7 + - - +
70A TYR* 3.6 3.8 + - + +
78A LEU* 4.1 21.3 - - + -
149A THR* 2.9 30.6 + - - +
189A ASN 3.5 4.9 - - - -
190A ILE* 4.0 28.0 - - + -
191A THR* 4.4 2.2 - - - -
51B LYS 5.5 1.7 - - - +
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Residues in contact with THR 69 (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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68A ALA* 1.3 70.8 - - - +
70A TYR* 1.3 58.9 + - - +
71A ASN* 3.4 22.4 - - - +
188A ALA* 3.1 7.0 - - - +
189A ASN* 2.7 56.3 + - + +
191A THR* 4.6 8.2 + - - +
9B THR* 5.1 4.3 + - - -
51B LYS* 5.9 6.8 - - + +
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Residues in contact with TYR 70 (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 TRP* 4.8 1.6 - + - -
68A ALA* 3.6 5.1 + - + +
69A THR* 1.3 74.6 - - - +
71A ASN* 1.3 69.7 + - - +
72A PRO* 3.5 32.0 - - + +
76A SER* 2.6 50.6 + - - -
77A TYR* 3.0 18.0 + - - -
78A LEU* 3.8 18.6 - - + -
96A SER* 3.6 31.4 - - - -
97A TRP* 3.6 12.4 - - - -
149A THR* 4.1 19.2 - - + +
179A VAL* 4.2 12.1 - - + -
187A SER 4.3 0.7 - - - -
188A ALA* 4.2 13.7 - - + -
53B ASN* 5.6 2.1 - - - +
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.4 30.7 - - - +
70A TYR* 1.3 78.2 - - - +
72A PRO* 1.3 65.2 - - - +
73A ASN* 3.9 7.6 + - - +
186A GLY* 3.6 2.4 - - - -
187A SER* 2.8 47.7 + - - +
188A ALA* 5.7 0.2 - - - +
53B ASN* 4.2 15.9 - - - +
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Residues in contact with PRO 72 (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 TRP* 4.3 3.6 - - + -
70A TYR* 3.5 37.9 - - + +
71A ASN* 1.3 92.2 - - - +
73A ASN* 1.3 63.5 + - - +
74A GLY 3.4 6.5 - - - +
76A SER* 3.5 32.1 - - - +
97A TRP 4.3 1.3 - - - +
98A GLY* 3.9 15.9 - - - -
185A SER 4.2 0.4 - - - +
186A GLY* 4.1 7.6 - - - -
187A SER 4.1 0.2 - - - -
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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