Contacts of the strand formed by residues 53 - 61 (chain L) in PDB entry 1CWD
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48L PHE* 4.0 16.8 - - - -
49L ASP* 2.6 43.9 + - - +
50L GLN 4.8 0.6 + - - -
51L ASN 3.7 0.4 - - - -
52L GLN* 1.3 74.5 - - - +
54L GLU* 1.3 63.2 + - - -
55L VAL* 3.3 1.2 + - - +
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Residues in contact with GLU 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 4.4 13.1 - - + +
26L HIS* 2.9 36.5 - - - -
46L ARG* 3.2 40.3 + - - +
47L ASP 3.6 1.9 - - - +
48L PHE* 3.5 18.6 - - - -
52L GLN 4.3 1.4 + - - +
53L GLY* 1.3 69.4 - - - -
55L VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 4.6 2.0 - - - -
46L ARG* 3.4 9.6 - - - +
47L ASP* 2.9 43.7 + - + +
48L PHE 4.4 1.1 - - - -
49L ASP* 4.0 16.6 - - + +
52L GLN* 3.6 35.0 - - + +
53L GLY 3.6 1.8 - - - +
54L GLU* 1.3 77.9 - - - +
56L VAL* 1.3 66.1 + - - +
57L LYS* 4.1 27.1 - - + +
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Residues in contact with VAL 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L GLU* 4.1 20.6 - - + +
19L LEU* 3.8 35.7 - - + -
20L LEU* 3.7 35.3 - - + +
45L VAL 3.2 10.3 - - - +
46L ARG* 4.4 2.2 - - + -
55L VAL* 1.3 78.0 - - - +
57L LYS* 1.3 66.6 + - - +
58L HIS* 3.4 35.4 + - + -
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Residues in contact with LYS 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L LEU 3.6 1.3 - - - +
44L SER* 3.2 5.9 - - - -
45L VAL* 2.9 36.1 + - + +
47L ASP* 4.4 8.4 + - + -
48L PHE 5.2 3.2 + - - -
49L ASP* 4.7 12.4 + - - -
55L VAL* 4.0 24.0 - - + +
56L VAL* 1.3 75.0 - - - +
58L HIS* 1.3 63.2 + - - +
59L TYR* 4.1 17.7 - - + -
95L CYS* 4.1 29.4 - - + +
6P GLU* 3.4 37.3 + - - +
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Residues in contact with HIS 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ARG* 3.2 48.0 - - + +
15L ALA* 4.9 0.4 - - + -
16L GLU* 2.8 34.0 + - + +
32L ARG* 3.3 16.6 + - - +
42L SER* 5.9 0.2 - - - -
43L LEU 3.5 2.7 - - - +
44L SER* 2.7 29.9 + - - -
56L VAL* 3.4 28.3 + - + +
57L LYS* 1.3 76.2 + - - +
59L TYR* 1.3 58.8 - - - +
4P ASP 4.6 2.0 - - - +
5P PM3 3.5 9.5 - - + -
6P GLU* 2.8 35.2 + - - +
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Residues in contact with TYR 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L SER* 3.4 5.9 - - - -
43L LEU* 2.8 46.3 + - + +
45L VAL* 3.9 24.9 - - + -
57L LYS* 4.1 9.3 - - + +
58L HIS* 1.3 74.6 - - - +
60L LYS* 1.3 60.8 + - - +
61L ILE 3.7 0.2 + - - -
71L ILE* 4.3 20.6 - - + -
93L GLY 5.2 0.9 - - - -
94L LEU* 4.0 24.7 - - + -
95L CYS* 2.8 44.7 + - - +
5P PM3 3.7 4.7 - - - -
6P GLU* 3.3 37.4 - - + +
7P GLU 4.9 1.1 - - - -
8P VAL* 3.7 28.3 - - + -
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Residues in contact with LYS 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L SER* 3.0 27.6 + - - +
41L PHE 2.8 27.5 + - - +
42L SER* 3.8 12.1 - - - -
59L TYR* 1.3 71.7 - - - +
61L ILE* 1.3 73.6 + - - +
62L ARG* 3.7 25.9 + - - +
71L ILE* 3.9 20.6 - - - +
5P PM3 3.6 42.5 - - + +
6P GLU 5.6 0.4 + - - -
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Residues in contact with ILE 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L ILE* 3.9 31.4 - - + -
41L PHE* 3.3 38.7 + - + +
42L SER 4.4 8.3 - - - -
43L LEU* 4.5 9.4 - - + +
59L TYR 3.7 0.6 + - - -
60L LYS* 1.3 86.7 + - - +
62L ARG* 1.3 63.8 + - - +
63L ASN* 3.9 5.9 - - - +
69L PHE* 3.6 37.9 - - + -
70L TYR 3.7 7.6 - - - +
71L ILE* 3.9 20.2 - - + -
80L LEU* 4.4 6.1 - - + -
83L LEU* 4.1 13.0 - - + -
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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