Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 1WD5
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 VAL 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 6.2 1.3 - - + -
52A VAL* 3.8 22.3 + - + +
53A LEU* 1.3 82.7 - - - +
55A ARG* 1.3 73.8 + - - +
70A VAL 3.3 10.8 - - - +
71A GLY* 4.2 0.4 - - - -
102A LEU* 3.8 8.4 - - - +
135A SER* 4.5 4.7 - - - +
138A ALA* 4.1 8.5 - - + +
139A ALA* 3.8 30.7 - - + +
142A VAL* 3.6 37.9 - - + -
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Residues in contact with ARG 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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54A VAL* 1.3 81.4 - - - +
56A LYS* 1.3 63.5 + - - +
69A ALA* 3.2 6.4 - - - +
70A VAL* 3.0 46.3 + - + +
98A GLN* 2.8 54.3 + - + +
101A VAL* 3.7 32.1 - - - +
102A LEU* 3.9 18.8 - - + -
138A ALA* 4.3 5.2 - - - -
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Residues in contact with LYS 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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55A ARG* 1.3 78.5 + - - +
57A VAL* 1.3 61.6 + - - +
58A GLY* 3.8 11.4 + - - +
63A PRO* 2.9 30.9 + - - +
64A GLU* 3.7 21.4 + - - +
66A ALA* 3.6 30.3 - - + -
68A GLY 3.9 5.6 - - - +
98A GLN* 3.3 25.3 + - - +
134A ALA* 4.4 28.6 - - - +
135A SER* 5.8 1.1 - - - -
138A ALA* 4.1 17.5 - - + +
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Residues in contact with VAL 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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55A ARG 4.5 0.2 - - - +
56A LYS* 1.3 73.9 - - - +
58A GLY* 1.3 62.1 + - - +
66A ALA* 3.7 1.4 - - - -
67A LEU* 2.9 26.0 + - + -
68A GLY* 3.0 20.3 + - - +
69A ALA* 3.9 11.9 - - - +
70A VAL* 3.7 30.7 - - + +
76A LEU* 4.0 10.3 - - + -
78A LEU* 5.5 0.7 - - + -
91A LEU* 4.6 24.7 - - + +
94A GLU* 3.3 27.8 - - + -
95A ALA* 4.4 7.2 - - - -
98A GLN* 4.5 3.8 - - + -
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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 LYS* 3.8 6.6 + - - +
57A VAL* 1.3 78.7 - - - +
59A ALA* 1.3 59.7 + - - -
63A PRO* 3.7 20.2 - - - -
65A PHE 3.4 9.2 - - - -
67A LEU* 4.4 3.1 - - - +
90A TYR* 2.8 29.7 + - - -
94A GLU* 3.0 17.8 + - - +
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Residues in contact with ALA 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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58A GLY* 1.3 73.3 - - - -
60A PRO* 1.3 79.3 - - + +
61A GLY 3.2 0.9 + - - -
62A ASN* 3.0 28.5 + - + +
63A PRO* 3.7 2.4 - - - +
65A PHE* 2.8 32.3 + - + +
67A LEU* 3.6 18.6 - - + +
85A TYR* 5.1 4.7 - - + -
90A TYR* 3.3 7.0 + - - -
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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