Contacts of the strand formed by residues 85 - 93 (chain A) in PDB entry 5AYZ
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 ALA 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TRP* 3.3 8.7 - - - -
48A ALA* 2.7 48.5 + - + -
75A LEU* 4.6 12.8 - - + -
81A LEU* 5.4 0.4 - - + -
82A VAL 3.4 23.2 + - - +
84A VAL* 1.3 72.6 - - - +
86A ARG* 1.3 60.7 + - - +
87A VAL* 3.4 6.3 - - + +
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Residues in contact with ARG 86 (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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45A ALA* 3.8 27.1 - - + +
46A LEU 3.6 6.5 - - - +
47A TRP* 3.4 36.0 - - + -
74A PHE* 3.7 43.7 - - + +
75A LEU* 4.8 3.6 - - - +
85A ALA* 1.3 71.6 - - - +
87A VAL* 1.3 60.1 + - - +
88A ALA 4.3 4.9 - - - +
89A GLU* 4.7 6.1 + - - +
286A PHE* 4.4 28.1 - - - +
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Residues in contact with VAL 87 (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 LEU* 2.9 31.3 + - + +
47A TRP 4.3 0.9 - - - -
48A ALA* 3.6 27.1 - - + +
54A LEU* 4.7 15.7 - - + -
73A TRP* 3.7 17.1 - - + -
74A PHE* 2.8 26.1 + - - -
75A LEU* 3.7 25.2 + - + -
81A LEU* 4.6 2.2 - - + -
85A ALA 3.4 18.2 - - - +
86A ARG* 1.3 73.7 - - - +
88A ALA* 1.3 61.4 + - - +
281A PHE* 4.8 3.4 - - + -
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Residues in contact with ALA 88 (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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45A ALA* 3.6 6.1 - - - +
46A LEU* 3.0 37.0 + - + +
60A PHE* 5.2 1.1 - - + -
71A VAL* 4.0 10.8 - - + -
72A SER 3.1 15.0 - - - +
73A TRP* 3.6 25.6 - - + -
74A PHE* 3.6 13.1 - - - -
86A ARG* 4.3 1.0 - - - +
87A VAL* 1.3 81.5 - - - +
89A GLU* 1.3 62.4 + - - +
90A VAL* 5.2 0.2 - - + -
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Residues in contact with GLU 89 (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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43A GLN* 4.5 2.9 - - + +
44A ALA 3.2 13.0 - - - +
70A GLN 3.8 0.3 - - - +
71A VAL* 3.4 4.7 - - - +
72A SER* 2.8 33.1 + - - +
74A PHE* 3.9 19.3 - - + -
86A ARG* 4.7 6.1 + - - +
88A ALA* 1.3 73.2 - - - +
90A VAL* 1.3 70.0 + - - +
91A ARG* 2.3 51.1 + - - +
286A PHE* 3.7 25.1 - - + -
288A LYS* 4.1 12.3 + - - -
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Residues in contact with VAL 90 (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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43A GLN* 3.2 4.7 - - - -
44A ALA* 2.8 39.8 + - + +
60A PHE* 3.7 28.9 - - + -
64A PHE* 3.8 28.7 - - + -
69A CYS* 4.2 2.7 - - + -
70A GLN 3.3 11.2 - - - +
71A VAL* 4.3 4.5 - - + -
88A ALA* 5.2 1.8 - - + -
89A GLU* 1.3 79.8 - - - +
91A ARG* 1.3 64.3 + - - +
97A LEU* 3.6 25.0 - - + +
283A LEU* 3.9 20.6 - - + -
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Residues in contact with ARG 91 (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 3.3 11.0 - - - +
43A GLN* 4.2 9.6 - - + -
69A CYS* 3.0 5.7 - - - +
70A GLN* 2.8 68.7 + - - +
71A VAL 4.4 1.6 + - - -
72A SER* 3.0 36.5 + - - +
89A GLU* 2.3 55.8 + - - +
90A VAL* 1.3 76.2 - - - +
92A GLY* 1.3 59.7 + - - +
97A LEU* 3.7 3.8 - - - -
288A LYS* 6.5 0.2 - - - +
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Residues in contact with GLY 92 (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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41A PRO* 4.3 4.2 - - - +
42A SER* 2.8 32.7 + - - +
68A ASN 4.3 3.1 - - - -
69A CYS* 3.8 9.2 - - - -
70A GLN* 5.1 1.8 - - - -
91A ARG* 1.3 74.3 - - - +
93A PRO* 1.3 78.7 - - - +
94A ALA 3.4 0.2 + - - -
97A LEU* 3.7 5.6 - - - +
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Residues in contact with PRO 93 (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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39A ALA* 3.4 22.0 - - + +
40A GLY 3.7 4.5 - - - +
41A PRO* 4.2 2.2 - - + -
67A LEU 4.8 0.7 - - - +
68A ASN* 3.8 18.2 - - + +
69A CYS* 4.3 4.9 - - - -
92A GLY* 1.3 83.1 - - - +
94A ALA* 1.3 66.2 + - - +
95A HIS* 3.2 21.5 - - + -
96A CYS* 2.9 24.7 + - + +
97A LEU* 3.1 10.9 + - - +
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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