Contacts of the strand formed by residues 57 - 66 (chain A) in PDB entry 1CF5
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 TYR 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASP* 5.1 1.6 - - - -
7A SER* 3.6 28.6 + - - -
53A THR* 3.4 15.0 - - + +
54A SER 2.8 9.7 + - - -
55A TYR 4.1 10.8 - - - -
56A ALA* 1.3 87.9 - - - +
58A GLU* 1.3 63.0 + - - +
59A THR* 3.5 8.7 + - - -
138A PHE* 5.4 0.7 - - - -
2C NAG 3.1 33.2 - - + +
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Residues in contact with GLU 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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53A THR* 3.2 3.3 - - - -
54A SER* 2.8 36.7 + - - +
56A ALA* 3.9 21.1 - - - +
57A TYR* 1.3 79.2 - - - +
59A THR* 1.3 59.0 + - - +
134A ILE* 3.3 15.3 - - + +
135A THR* 2.8 36.5 + - - +
138A PHE* 3.7 46.4 - - + -
139A TYR* 4.0 12.6 + - + +
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Residues in contact with THR 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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51A ASN* 3.1 28.5 - - - +
52A LEU 3.4 3.4 - - - +
53A THR* 2.9 24.2 + - - +
57A TYR 3.5 7.0 + - - -
58A GLU* 1.3 72.4 - - - +
60A ILE* 1.3 66.7 + - - +
61A SER* 6.0 0.9 - - - -
75A ARG* 4.5 13.1 + - - +
77A ARG 4.7 3.1 + - - -
138A PHE* 4.0 14.1 - - - -
1C NAG 4.4 9.5 - - - +
2C NAG 3.9 11.6 + - - -
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Residues in contact with ILE 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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50A LEU 3.8 0.3 - - - +
51A ASN* 3.9 3.1 - - - +
52A LEU* 2.9 46.3 + - + +
59A THR* 1.3 82.3 - - - +
61A SER* 1.3 60.3 + - - +
62A VAL* 4.2 16.6 - - + -
74A TYR* 4.5 9.2 - - + -
75A ARG 3.6 11.7 - - - +
76A THR* 4.8 2.7 - - - -
134A ILE* 4.0 24.9 - - + +
137A LEU* 3.7 33.4 - - + -
138A PHE* 3.9 35.4 - - + +
152A LEU* 5.0 2.7 - - + -
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Residues in contact with SER 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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1A ASP* 5.1 3.5 + - - -
49A LEU* 3.6 28.9 - - - +
50A LEU 3.4 8.7 + - - -
51A ASN* 4.8 5.9 - - - +
59A THR* 6.0 1.1 - - - -
60A ILE* 1.3 74.6 - - - +
62A VAL* 1.3 59.6 + - - +
74A TYR* 3.5 1.9 - - - +
75A ARG* 2.8 59.2 + - - +
95A PHE* 3.9 6.0 - - - -
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Residues in contact with VAL 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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48A ILE 3.9 0.2 - - - +
49A LEU* 3.3 5.6 - - - -
50A LEU* 2.8 40.8 + - + +
52A LEU* 3.7 28.5 - - + -
60A ILE* 4.2 15.9 - - + -
61A SER* 1.3 74.8 - - - +
63A ALA* 1.3 61.6 + - - +
64A ILE* 4.0 21.7 + - + -
71A VAL* 4.3 10.8 - - + -
73A ALA 3.8 3.4 - - - +
74A TYR* 4.0 13.0 - - + -
152A LEU* 4.1 24.9 - - + -
156A THR* 5.9 0.9 - - - +
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Residues in contact with ALA 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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47A PHE* 5.0 1.3 - - + -
48A ILE 3.6 3.6 - - - +
49A LEU* 3.8 14.1 - - + -
61A SER 4.3 0.2 + - - -
62A VAL* 1.3 72.7 - - - +
64A ILE* 1.3 63.3 + - - +
71A VAL* 3.3 5.2 - - - +
72A VAL* 2.9 33.8 + - + +
73A ALA 2.8 18.9 + - - +
94A LEU* 3.6 31.6 - - + -
95A PHE* 4.0 6.2 - - + -
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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
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21A PHE* 4.3 7.9 - - + -
25A LEU* 4.6 1.6 - - + -
47A PHE* 3.2 8.5 - - - -
48A ILE* 2.7 62.5 + - + +
50A LEU* 3.7 38.8 - - + -
62A VAL* 4.0 5.4 - - + -
63A ALA* 1.3 80.5 - - - +
65A ASP* 1.3 68.0 + - - +
66A VAL* 3.3 1.4 + - - +
69A VAL* 3.8 32.3 - - + +
70A TYR 3.4 7.2 - - - +
71A VAL* 4.0 24.7 - - + +
156A THR* 5.3 2.9 - - - +
157A ALA* 5.6 1.6 - - + -
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Residues in contact with ASP 65 (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 ARG* 3.4 33.2 + - - -
47A PHE* 4.0 9.2 - - + -
63A ALA 4.1 0.6 + - - -
64A ILE* 1.3 72.3 - - - +
66A VAL* 1.3 53.7 + - - +
67A THR* 2.7 37.2 + - - +
68A ASN* 2.9 36.7 + - - +
69A VAL 2.9 10.0 + - - -
70A TYR* 2.9 12.3 + - + +
72A VAL* 3.7 20.4 - - + +
87A PRO* 4.4 6.8 - - - +
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Residues in contact with VAL 66 (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 LEU* 3.6 20.1 - - + +
26A PRO* 3.8 30.6 - - + +
37A LEU* 3.6 25.6 - - - +
38A TYR* 4.9 3.4 + - + +
41A ILE* 4.3 16.8 - - + -
45A ARG 3.8 12.1 - - - +
46A ARG 3.0 25.6 + - - +
48A ILE* 3.0 37.7 - - + +
64A ILE 3.3 0.4 + - - +
65A ASP* 1.3 68.6 - - - +
67A THR* 1.3 61.4 + - - +
68A ASN 3.1 2.8 + - - -
69A VAL 4.3 0.7 - - - -
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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