Contacts of the strand formed by residues 92 - 100 (chain I) in PDB entry 1LK3
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 92 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I LYS* 3.7 34.1 - - + -
39I GLN 3.4 14.6 - - - +
40I SER* 3.8 6.1 - - - +
41I HIS 5.0 2.0 - - - +
90I ASP 3.2 2.8 + - - -
91I SER* 1.3 77.2 - - - +
93I ASN* 1.3 61.3 + - - +
94I TYR* 3.7 12.4 - - + -
114I LEU* 3.7 8.5 - - - +
115I VAL 2.9 31.0 + - - +
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Residues in contact with ASN 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL 3.9 0.7 - - - +
38I LYS* 3.7 0.9 - - - -
39I GLN* 3.0 47.0 + - + +
92I ALA* 1.3 73.3 - - - +
94I TYR* 1.3 62.3 + - - +
95I SER* 4.1 4.9 + - - -
111I GLN 4.7 2.0 + - - -
112I GLY* 3.9 21.5 - - - -
113I THR 3.4 5.5 + - - -
114I LEU* 3.9 25.1 + - + +
42M GLN* 4.2 16.6 - - - +
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Residues in contact with TYR 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 2.8 17.0 - - - +
20I LEU* 3.7 18.4 - - + -
36I TRP* 4.8 0.7 - - + -
37I VAL 3.3 6.5 - - - +
38I LYS* 3.6 27.8 + - + +
48I ILE* 3.7 19.5 - - + -
64I PHE* 5.6 1.9 - + - -
67I LYS* 6.0 0.5 - - - +
81I MET* 3.6 23.1 - - + -
83I LEU* 3.7 27.0 - - + +
90I ASP* 2.7 41.9 + - - +
92I ALA* 3.7 15.5 - - + -
93I ASN* 1.3 72.2 - - - +
95I SER* 1.3 61.4 + - - +
112I GLY* 3.4 0.2 - - - -
113I THR* 2.7 28.8 + - - +
115I VAL* 3.5 29.4 - - + -
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Residues in contact with SER 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 3.3 7.6 - - - +
36I TRP* 3.2 10.0 - - - -
37I VAL* 2.7 42.5 + - - +
39I GLN* 6.1 0.5 - - - +
93I ASN* 4.1 6.1 + - - -
94I TYR* 1.3 77.4 + - - +
96I CYS* 1.3 62.6 + - - +
109I TRP* 3.9 23.7 - - - -
110I GLY 4.7 0.4 - - - -
112I GLY* 3.9 3.5 - - - -
42M GLN* 2.8 33.3 + - - -
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Residues in contact with CYS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.0 10.5 - - - -
6I GLN* 3.2 27.9 - - - +
22I CYS* 2.0 54.3 - - + -
34I ILE* 4.2 4.0 - - + -
35I HIS 3.1 11.0 - - - +
36I TRP* 4.0 14.1 - - + -
95I SER* 1.3 75.6 - - - +
97I THR* 1.3 64.4 + - - +
110I GLY 2.8 26.2 + - - -
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Residues in contact with THR 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 3.8 7.2 - - - -
34I ILE* 3.5 7.3 - - - +
35I HIS* 2.8 51.7 + - - +
37I VAL* 4.5 8.9 - - + +
95I SER 5.0 0.2 - - - +
96I CYS* 1.3 79.9 - - - +
98I ARG* 1.3 58.5 + - - +
106I PHE* 3.2 25.1 - - + -
108I TYR 3.3 11.7 - - - +
109I TRP* 3.5 43.7 - - + -
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Residues in contact with ARG 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I VAL* 3.9 12.6 - - - +
4I LEU* 3.7 12.7 - - + +
27I TYR* 3.4 57.8 - - + +
32I PHE* 3.4 55.0 - - + -
33I TYR 3.5 4.5 - - - +
34I ILE* 5.1 1.8 - - - -
97I THR* 1.3 74.3 - - - +
99I GLY* 1.3 62.7 + - - +
100I VAL* 4.3 5.9 + - - +
106I PHE* 4.1 11.7 - - - -
107I PRO* 4.2 19.2 - - - +
108I TYR* 3.3 49.7 + - + +
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Residues in contact with GLY 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I PHE* 3.5 7.7 - - - +
33I TYR* 2.8 42.1 + - - +
35I HIS* 3.9 20.3 + - - -
97I THR 3.9 0.6 + - - -
98I ARG* 1.3 76.4 - - - +
100I VAL* 1.3 67.8 + - - -
101I PRO 3.2 0.9 - - - -
103I ASN 4.4 4.9 - - - -
105I TRP 4.7 4.3 - - - -
106I PHE* 4.8 0.7 - - - -
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Residues in contact with VAL 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASN* 3.3 27.4 - - - +
32I PHE* 3.8 23.2 - - + -
33I TYR* 5.4 0.5 - - - -
35I HIS* 5.6 1.2 - - - -
98I ARG* 4.3 6.2 + - - +
99I GLY* 1.3 71.8 - - - -
101I PRO* 1.3 65.2 - - + +
102I GLY 3.2 0.3 + - - -
103I ASN* 2.8 61.3 + - + +
105I TRP 5.3 0.6 + - - -
107I PRO* 6.2 4.2 - - + +
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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