Contacts of the strand formed by residues 106 - 113 (chain W) in PDB entry 5L4K
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 LYS 106 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2W VAL* 3.9 36.0 - - + +
3W LEU 3.4 4.8 + - - +
4W GLU* 3.7 20.5 - - + +
5W SER* 2.7 29.8 + - - +
100W ARG* 4.4 0.4 - - - -
104W ASN* 3.3 21.4 + - - +
105W HIS* 1.3 76.4 + - - +
107W MET* 1.3 61.7 - - - +
108W ARG* 3.5 1.2 + - + -
137W ASN* 5.1 8.7 - - - +
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Residues in contact with MET 107 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W SER 4.2 1.6 - - - -
94W HIS* 5.6 1.3 - - - +
97W LEU* 4.1 39.9 - - + +
98W LYS* 4.3 14.4 - - + +
100W ARG* 3.4 40.8 - - - +
105W HIS 5.1 0.2 - - - +
106W LYS* 1.3 71.4 - - - +
108W ARG* 1.3 59.2 + - - +
134W GLU* 3.8 26.0 - - - +
135W LYS 3.7 14.5 + - - +
136W VAL* 4.0 14.6 - - - -
137W ASN* 2.8 37.3 + - - +
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Residues in contact with ARG 108 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 6.2 1.2 - - - +
4W GLU* 3.9 24.3 + - - +
5W SER 2.8 29.3 + - - +
6W THR* 3.3 3.5 - - - +
7W MET* 3.0 17.8 + - - +
40W LYS* 3.9 21.3 - - - +
97W LEU* 4.3 2.7 - - - +
106W LYS* 3.5 0.6 + - + +
107W MET* 1.3 74.7 - - - +
109W ILE* 1.3 64.6 + - - +
110W ILE* 3.9 14.8 - - + -
137W ASN* 3.3 40.9 + - - +
138W VAL 4.6 1.6 - - - +
139W ASP* 3.2 35.6 + - - -
166W THR* 3.7 23.6 + - - -
167W GLY 4.9 0.8 + - - -
168W SER* 5.5 0.2 - - - +
169W HIS* 4.1 4.9 - - - -
192W GLU* 4.9 11.8 + - - +
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Residues in contact with ILE 109 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W MET* 3.6 12.3 - - + +
9W CYS* 3.3 35.0 - - - -
90W ILE* 4.5 11.7 - - + -
93W ALA* 4.0 20.0 - - + -
94W HIS* 4.7 6.3 - - + -
97W LEU* 3.9 13.7 - - + -
108W ARG* 1.3 76.3 - - - +
110W ILE* 1.3 65.1 + - - +
111W ALA* 4.5 5.8 - - + -
131W LEU* 4.8 1.6 - - + -
136W VAL* 3.4 27.6 - - + -
137W ASN 2.9 13.2 + - - +
138W VAL* 4.1 15.0 - - + -
139W ASP 2.9 29.1 + - - +
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Residues in contact with ILE 110 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W THR* 3.7 24.7 - - + -
7W MET 2.6 12.3 + - - +
8W VAL* 3.3 6.9 - - + -
9W CYS 2.8 29.5 + - - +
36W VAL* 3.9 14.1 - - + -
40W LYS* 4.9 9.2 - - + +
108W ARG* 3.9 13.7 - - + -
109W ILE* 1.3 73.7 - - - +
111W ALA* 1.3 53.5 + - - +
112W PHE* 3.9 24.9 + - + -
139W ASP* 3.6 26.5 - - + +
141W ILE* 4.9 4.7 - - + -
187W PRO* 3.7 31.6 - - + -
188W ILE* 6.4 0.4 - - + -
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Residues in contact with ALA 111 (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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9W CYS* 3.7 22.2 - - + -
54W LEU* 5.3 0.7 - - + -
86W PHE* 5.0 7.0 - - + -
90W ILE* 5.6 1.8 - - + -
109W ILE* 4.5 6.5 - - + -
110W ILE* 1.3 73.8 - - - +
112W PHE* 1.3 56.6 + - - +
113W VAL* 4.1 9.6 + - + -
138W VAL* 4.6 8.1 - - + -
139W ASP 2.8 19.4 + - - +
140W ILE* 3.4 7.7 - - + +
141W ILE* 2.7 35.4 + - - +
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Residues in contact with PHE 112 (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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8W VAL* 4.1 8.1 - - + -
9W CYS 2.6 27.5 + - - +
10W VAL* 4.5 1.6 - - - -
11W ASP* 3.3 18.3 - - - +
29W GLN* 3.4 30.5 - - - +
32W ALA* 4.5 10.8 - - + -
33W VAL* 3.8 29.4 - - + -
36W VAL* 4.2 26.7 - - + -
54W LEU* 3.7 12.0 - - - +
110W ILE* 3.9 24.0 - - + -
111W ALA* 1.3 73.5 - - - +
113W VAL* 1.3 62.5 + - - +
141W ILE* 3.6 37.2 - - + +
143W PHE* 5.1 5.2 - + + -
187W PRO* 5.6 1.1 - - + -
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Residues in contact with VAL 113 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W ASP* 4.0 6.5 - - - -
25W ARG* 3.8 0.9 + - - -
54W LEU* 4.4 9.4 - - + -
84W ILE* 5.8 5.4 - - + -
86W PHE* 4.0 24.2 - - + -
111W ALA* 4.6 3.8 - - + +
112W PHE* 1.3 80.3 - - - +
114W GLY* 1.3 58.2 + - - +
140W ILE* 3.7 24.2 - - + -
141W ILE 3.2 16.0 + - - +
142W ASN* 3.3 26.9 - - - +
143W PHE 3.5 16.1 + - - +
144W GLY 4.2 1.6 - - - +
145W GLU* 3.2 17.6 - - - +
153W LEU* 4.7 3.8 - - + -
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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