Contacts of the strand formed by residues 103 - 107 (chain A) in PDB entry 4LKC
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLN* 3.0 23.1 + - - +
9A PRO* 2.7 29.6 + - + +
10A SER 3.3 4.9 - - - +
12A LEU* 3.7 28.7 - - + -
22A ILE* 3.6 29.6 - - + +
85A ALA 3.7 0.2 - - - +
86A THR* 3.3 5.1 - - - +
87A TYR* 2.9 38.4 + - - -
102A GLY* 1.3 71.3 + - - -
104A ARG* 1.3 62.9 + - - +
105A LEU 3.5 1.7 + - - -
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Residues in contact with ARG 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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10A SER 3.0 7.6 + - - +
11A SER* 3.3 21.7 + - - +
12A LEU* 3.0 28.8 + - - +
84A PHE* 5.8 4.3 - - - -
85A ALA 3.7 5.8 - - - +
86A THR* 4.1 17.6 - - + +
102A GLY 4.2 0.6 - - - -
103A THR* 1.3 70.5 - - - +
105A LEU* 1.3 62.4 + - - +
106A GLU* 3.6 29.6 + - - +
143A ARG* 6.3 0.6 - - - +
166A GLU* 4.8 14.6 + - - -
167A GLN* 5.2 3.8 + - - +
174A TYR* 3.3 32.5 + - - -
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Residues in contact with LEU 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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12A LEU* 3.6 31.6 - - + -
14A ALA* 4.5 2.0 - - + -
20A VAL* 4.3 11.2 - - + -
22A ILE* 5.0 2.0 - - + -
76A ILE* 3.7 30.1 - - + -
79A LEU* 3.9 28.3 - - + -
83A ASP 3.8 9.6 - - - +
84A PHE* 3.3 11.4 - - - +
85A ALA 2.8 33.8 + - - +
87A TYR* 3.7 20.0 - - + -
103A THR 3.5 1.0 + - - +
104A ARG* 1.3 76.1 + - - +
106A GLU* 1.3 74.2 + - - +
107A ILE* 4.6 2.2 - - + -
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Residues in contact with GLU 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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12A LEU 2.9 12.9 + - - +
13A SER* 2.5 30.6 + - - +
14A ALA 3.0 25.1 + - - +
104A ARG* 3.6 21.8 + - - +
105A LEU* 1.3 79.6 - - - +
107A ILE* 1.3 64.4 + - - +
108A LYS 3.9 0.2 - - - -
141A TYR* 2.9 21.6 + - - -
142A PRO* 5.9 0.2 - - - +
143A ARG* 4.4 8.1 + - - +
167A GLN* 3.4 9.2 - - - +
174A TYR* 2.6 39.2 + - - +
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Residues in contact with ILE 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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14A ALA 3.3 6.3 - - - +
16A VAL* 3.8 26.7 - - + +
79A LEU* 3.8 24.7 - - + -
80A GLN 3.4 18.4 - - - +
81A PRO* 3.4 22.0 - - + +
83A ASP* 4.0 4.0 - - + -
84A PHE* 3.6 25.6 - - + +
105A LEU* 4.6 2.9 - - + -
106A GLU* 1.3 71.8 - - - +
108A LYS* 1.3 76.3 + - - +
109A ARG* 4.2 2.1 - - - +
141A TYR* 3.6 6.9 + - - -
167A GLN* 2.8 34.3 + - - +
172A SER* 4.1 17.4 - - - +
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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