Contacts of the strand formed by residues 102 - 110 (chain A) in PDB entry 1L8F
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 THR 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASN* 2.9 21.5 + - - +
67A LEU* 3.4 22.5 - - - +
68A SER 3.2 18.4 + - - -
91A LEU 3.1 7.0 - - - +
92A THR* 3.6 21.8 - - + +
93A PHE* 5.0 0.7 - - - -
100A GLY 4.1 7.6 - - - +
101A LYS* 1.3 77.0 - - - +
103A MET* 1.3 64.1 + - - +
172A TRP* 3.4 6.3 - - - -
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Residues in contact with MET 103 (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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60A PRO* 3.9 16.2 - - + -
67A LEU* 4.2 1.5 - - - +
68A SER* 3.1 18.2 - - - +
69A TYR 4.1 3.1 - - - +
70A GLY* 3.9 16.2 - - - -
71A PHE 5.1 1.1 - - - +
90A ALA* 4.6 0.2 - - - -
91A LEU* 2.7 49.0 + - + +
93A PHE* 4.0 32.1 - - + -
102A THR* 1.3 79.4 - - - +
104A VAL* 1.3 61.6 + - - +
105A VAL* 3.7 19.3 - - + -
121A LEU* 4.3 13.2 - - + -
168A TRP* 3.6 37.2 - - + -
172A TRP* 4.4 1.6 - - + -
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Residues in contact with VAL 104 (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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67A LEU* 4.4 9.2 - - + -
68A SER 3.0 5.7 + - - -
69A TYR* 3.3 28.5 - - + +
70A GLY 2.9 23.4 + - - +
88A CYS* 4.2 10.5 - - + -
89A TYR 3.3 9.6 - - - +
90A ALA* 4.6 12.8 - - + -
103A MET* 1.3 74.2 - - - +
105A VAL* 1.3 61.9 + - - +
186A VAL* 4.3 10.3 - - + -
189A PRO* 3.8 31.0 - - + -
192A LEU* 3.8 8.2 - - + +
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Residues in contact with VAL 105 (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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70A GLY 3.3 11.0 - - - +
71A PHE* 4.5 7.0 - - - +
72A ALA* 4.8 2.2 - - + -
74A THR* 5.6 0.2 - - + -
87A ALA 3.8 0.5 - - - +
88A CYS* 3.1 3.1 - - - -
89A TYR* 2.8 42.4 + - + +
91A LEU* 3.7 17.9 - - + -
103A MET* 3.7 31.9 - - + -
104A VAL* 1.3 79.3 - - - +
106A GLN* 1.3 61.7 + - - +
107A SER 4.0 0.3 + - - -
119A PHE* 3.4 38.6 - - + -
121A LEU* 4.2 9.6 - - + -
192A LEU* 4.4 2.5 - - - -
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Residues in contact with GLN 106 (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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70A GLY 3.0 7.7 + - - -
71A PHE* 3.4 15.4 - - + +
72A ALA 3.1 21.8 + - - -
86A CYS* 3.1 21.5 + - - +
87A ALA 3.3 9.9 - - - +
88A CYS* 3.6 13.7 - - - -
105A VAL* 1.3 76.1 - - - +
107A SER* 1.3 72.7 + - - +
108A THR* 3.4 3.2 + - + +
188A CYS* 3.9 1.2 - - - -
192A LEU* 3.5 17.2 - - + +
193A VAL* 3.8 11.1 - - - +
196A THR* 2.7 36.0 + - - +
198A CYS 2.9 27.9 + - - -
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Residues in contact with SER 107 (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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16A CYS* 4.4 0.2 - - - -
72A ALA 3.3 6.5 - - - -
74A THR* 2.8 36.1 + - - -
84A TRP* 3.2 34.1 + - - -
85A CYS* 4.1 1.4 - - - -
86A CYS* 2.8 30.7 + - - -
87A ALA 2.8 11.8 + - - -
89A TYR* 4.3 6.1 - - - -
105A VAL 4.0 0.8 + - - -
106A GLN* 1.3 73.7 - - - +
108A THR* 1.3 58.9 + - - +
109A SER 3.4 6.9 + - - -
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Residues in contact with THR 108 (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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14A PRO* 3.1 26.3 - - - +
16A CYS* 3.1 24.7 + - - +
28A VAL* 4.0 17.3 - - + -
58A HIS* 5.1 4.9 - - + +
71A PHE* 3.8 30.7 - - + +
72A ALA 2.9 11.5 + - - -
106A GLN* 3.9 5.2 - - - +
107A SER* 1.3 78.1 - - - +
109A SER* 1.3 61.4 + - - +
122A ASN* 4.3 14.7 + - - -
196A THR* 3.8 18.4 - - + -
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Residues in contact with SER 109 (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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8A TYR* 4.1 11.8 + - - -
13A LYS 5.1 0.2 + - - -
14A PRO* 4.0 6.8 - - - +
15A SER* 3.1 30.2 + - - -
16A CYS* 3.5 3.9 - - - -
72A ALA 3.6 2.0 + - - -
73A ALA* 3.6 18.8 - - - +
74A THR* 2.8 21.5 + - - +
84A TRP* 3.9 0.7 + - - -
107A SER* 3.4 8.5 + - - -
108A THR* 1.3 86.1 + - - +
110A THR* 1.3 70.0 + - - +
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Residues in contact with THR 110 (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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15A SER* 2.9 10.1 + - - -
73A ALA* 4.2 5.4 - - - +
74A THR 3.3 2.9 - - - -
81A GLU* 2.7 33.4 + - + +
84A TRP* 3.0 36.3 + - + -
109A SER* 1.3 79.5 + - - +
111A GLY* 1.3 74.5 + - - +
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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