Contacts of the strand formed by residues 53 - 61 (chain A) in PDB entry 1F5F
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLU* 1.3 78.9 - - - +
54A VAL* 1.3 64.8 + - - -
70A GLY* 3.2 2.9 - - - -
71A LEU* 2.9 33.5 + - - +
157A LEU* 4.2 6.1 - - - +
158A VAL 3.5 10.5 - - - -
159A PRO 3.4 12.8 - - - -
160A ALA 3.7 3.6 - - - -
161A LEU* 3.9 9.6 - - - +
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Residues in contact with VAL 54 (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 LEU* 5.4 0.3 - - - +
53A GLY* 1.3 75.2 - - - -
55A ILE* 1.3 63.7 + - - +
56A PHE 3.5 27.8 - - - +
68A MET* 4.0 11.4 - - + -
69A LEU 3.9 4.7 - - - +
70A GLY* 4.2 1.3 - - - -
144A GLY* 3.5 14.6 - - - -
145A GLY* 3.8 25.4 - - - +
146A LEU* 3.7 23.8 - - + -
157A LEU* 4.1 10.8 - - + -
159A PRO* 2.8 34.1 + - + +
161A LEU* 3.7 13.0 - - - +
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Residues in contact with ILE 55 (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 LEU* 4.3 19.0 - - + +
44A PHE* 3.7 36.3 - - + -
46A VAL* 4.9 13.9 - - + -
54A VAL* 1.3 70.9 - - - +
56A PHE* 1.3 64.2 + - + +
69A LEU* 2.8 35.0 + - + +
70A GLY* 3.8 6.7 - - - +
71A LEU* 4.3 24.0 - - + -
76A PRO* 6.5 0.2 - - + -
95A LEU* 5.4 3.6 - - + -
103A VAL* 5.6 1.6 - - + -
143A LEU* 3.8 2.3 - - - +
144A GLY* 2.9 20.9 + - - -
161A LEU* 3.4 22.9 - - + -
165A LEU* 5.0 4.0 - - + +
170A TRP* 5.5 1.1 - - + -
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Residues in contact with PHE 56 (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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42A SER* 5.1 2.0 - - - -
44A PHE* 3.9 12.6 - + - -
54A VAL* 3.5 7.1 - - - +
55A ILE* 1.3 80.8 - - + +
57A TYR* 1.3 71.3 + - - +
67A PHE* 3.8 31.4 - + - -
68A MET* 3.6 1.7 - - - -
69A LEU* 2.9 57.6 + - + +
105A VAL* 4.1 13.7 - - + -
141A ILE* 4.2 6.7 - - + -
142A ALA 3.1 13.7 - - - +
143A LEU* 3.9 14.8 - - + -
144A GLY 4.3 0.2 - - - +
170A TRP* 3.5 31.4 - + + -
253A DHT 4.0 26.7 - - + -
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Residues in contact with TYR 57 (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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56A PHE* 1.3 77.5 - - - +
58A GLY* 1.3 60.9 + - - +
59A ASP* 2.6 48.0 + - + +
62A PRO* 3.7 3.8 - - - +
66A TRP* 3.7 13.5 - + + +
67A PHE 3.3 16.8 - - - +
68A MET* 4.3 0.9 - - + +
141A ILE* 3.4 6.9 - - - +
142A ALA* 2.8 30.6 + - + +
145A GLY 3.4 18.8 - - - +
146A LEU* 3.8 26.0 - - + -
147A LEU* 3.7 37.3 - - + +
148A PHE* 3.5 40.9 - + - -
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Residues in contact with GLY 58 (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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56A PHE* 4.6 1.4 - - - -
57A TYR* 1.3 78.5 - - - +
59A ASP* 1.4 62.2 + - - +
66A TRP* 3.3 2.9 - - - +
67A PHE* 2.8 37.3 + - - +
140A ARG 3.1 11.4 - - - -
141A ILE* 3.8 12.8 - - - -
253A DHT 3.9 15.0 - - - +
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Residues in contact with ASP 59 (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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57A TYR* 2.6 32.7 + - - +
58A GLY* 1.4 74.7 - - - +
60A THR* 1.3 65.6 + - - +
61A ASN* 3.4 7.7 + - - +
62A PRO* 3.4 12.6 - - - +
65A ASP 3.2 13.5 - - - +
66A TRP* 3.8 1.1 - - + -
138A ILE 5.5 0.2 - - - +
139A MET* 3.1 9.0 - - - +
140A ARG* 2.8 79.0 + - - +
253A DHT 4.3 4.5 - - - +
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Residues in contact with THR 60 (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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34A LEU* 3.6 20.4 - - + -
59A ASP* 1.3 75.8 - - - +
61A ASN* 1.3 65.7 + - - +
65A ASP* 2.9 38.5 + - - +
131A LEU* 5.3 1.6 - - + -
136A HIS* 3.6 25.0 - - + +
137A PRO* 5.6 1.2 - - - +
138A ILE 3.4 18.5 + - - +
139A MET* 3.5 32.1 - - + -
253A DHT 4.0 8.8 - - + +
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Residues in contact with ASN 61 (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 ASP* 3.4 6.0 - - - +
60A THR 1.3 84.5 + - - +
62A PRO* 1.3 71.1 - - - +
63A LYS* 3.2 13.6 + - - +
64A ASP* 3.1 31.2 + - + +
65A ASP* 2.8 53.7 + - - +
66A TRP* 3.9 0.5 - - - +
136A HIS* 5.2 3.9 - - + -
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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