Contacts of the strand formed by residues 97 - 103 (chain W) in PDB entry 5A0Q
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 97 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45W GLY* 3.5 3.3 - - - -
46W ALA 2.9 32.5 + - - +
47W GLY* 4.8 0.4 - - - -
52W THR* 4.1 0.2 + - - -
87W LEU* 5.3 0.9 - - - -
95W GLY 5.4 0.2 - - - +
96W ALA* 1.3 75.5 - - - +
98W LEU* 1.3 61.7 + - - +
113W ILE 3.4 13.7 - - - +
114W TYR* 4.2 1.6 - - + -
115W PRO* 3.8 24.7 - - + -
127W MET* 3.2 25.9 - - + +
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Residues in contact with LEU 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43W CYS* 3.1 30.3 - - - -
44W CYS 3.3 9.6 - - - +
45W GLY* 3.8 1.1 - - - -
52W THR* 3.3 27.6 - - - +
55W THR* 4.2 18.2 - - + -
56W THR* 3.4 16.8 - - - +
83W LEU* 3.5 30.7 - - + -
87W LEU* 4.4 11.0 - - + +
96W ALA 4.9 2.2 - - - +
97W ALA* 1.3 75.8 - - - +
99W VAL* 1.3 62.0 + - - +
100W LEU 4.0 0.9 - - - -
113W ILE* 2.9 45.1 + - + +
127W MET* 3.3 2.8 - - - +
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Residues in contact with VAL 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W ILE* 3.6 30.5 - - + -
4W ALA 4.6 6.1 - - - +
14W LEU* 4.1 12.3 - - + +
42W TYR 4.1 0.2 - - - +
43W CYS* 3.4 2.8 - - - -
44W CYS* 3.0 37.4 + - + +
98W LEU* 1.3 75.1 - - - +
100W LEU* 1.4 58.4 + - - +
101W GLY 4.0 0.5 + - - -
110W LEU* 3.4 30.3 - - + -
111W TYR 3.7 4.3 - - - +
112W SER* 4.5 1.1 - - - +
125W VAL* 3.4 23.8 - - + -
127W MET* 3.9 17.7 - - + +
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Residues in contact with LEU 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37W ILE* 3.6 24.2 - - + -
41W ILE* 3.5 19.5 - - + -
42W TYR 3.7 4.0 - - - +
43W CYS* 4.2 4.3 - - + -
76W VAL* 3.4 33.4 - - + -
79W ALA* 3.6 23.8 - - + -
80W ASN* 3.8 20.4 - - - +
83W LEU* 3.4 26.7 - - + -
98W LEU 4.0 1.2 - - - -
99W VAL* 1.4 72.0 - - - +
101W GLY* 1.3 58.8 + - - +
110W LEU* 3.3 6.4 - - - +
111W TYR 2.9 33.5 + - - +
113W ILE* 4.3 7.6 - - + +
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Residues in contact with GLY 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W ILE* 4.5 11.0 - - - -
14W LEU* 4.5 6.3 - - - +
41W ILE* 3.2 5.9 - - - +
42W TYR* 3.0 33.3 + - - +
99W VAL 4.0 1.2 + - - -
100W LEU* 1.3 77.0 - - - +
102W GLY* 1.3 58.4 + - - -
109W HIS 3.4 8.7 - - - -
110W LEU* 4.2 9.4 - - - -
178W ILE* 4.6 6.4 - - - +
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Residues in contact with GLY 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W ILE* 3.1 7.3 - - - +
40W ASN 3.9 6.3 - - - -
41W ILE* 3.5 19.5 - - - -
76W VAL* 3.4 12.4 - - - +
101W GLY* 1.3 74.4 - - - -
103W VAL* 1.3 63.6 + - - -
109W HIS 3.0 30.2 + - - +
178W ILE* 4.0 4.3 - - - -
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Residues in contact with VAL 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W ASP 4.6 2.5 - - - +
11W GLY* 4.3 7.9 - - - -
12W ILE* 3.7 3.4 - - + -
40W ASN* 4.1 26.4 + - - +
41W ILE* 4.4 0.6 - - - +
73W LEU* 5.5 1.4 - - - +
76W VAL* 3.7 3.3 - - - +
102W GLY* 1.3 76.1 - - - +
104W ASP* 1.3 72.4 + - - +
107W GLY* 4.0 10.5 - - - -
108W PRO* 3.7 22.0 - - + -
178W ILE* 3.4 28.3 - - + +
179W SER* 4.6 4.5 - - - -
180W LYS* 4.3 35.0 - - + +
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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