Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 1K11
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 GLY 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 3.5 3.5 - - - +
115A SER* 2.8 35.0 + - - -
116A LYS 3.7 0.6 - - - -
117A TYR* 1.3 81.9 - - - +
119A ILE* 1.3 65.8 + - - -
120A LYS* 3.7 8.5 + - - +
132A ARG* 6.2 1.6 - - - -
133A HIS 3.2 13.9 - - - -
134A ALA* 4.3 0.9 - - - -
135A LEU* 3.8 6.9 - - - +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A MET* 3.8 33.7 - - + -
113A GLY 3.7 1.8 - - - +
114A VAL* 3.9 33.4 - - + -
115A SER 4.2 6.1 - - - +
118A GLY* 1.3 75.8 - - - +
120A LYS* 1.3 61.2 + - - +
121A VAL* 4.9 1.3 - - + -
132A ARG* 3.8 0.3 - - - -
133A HIS* 2.8 41.3 + - + +
135A LEU* 4.1 11.0 - - + -
138A ILE* 4.1 26.9 - - + -
157A LEU* 3.9 15.7 - - + -
183A ILE* 3.9 19.3 - - + -
186A VAL* 5.3 0.2 - - + -
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Residues in contact with LYS 120 (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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112A MET* 3.2 10.0 - - - +
113A GLY* 2.8 39.4 + - - +
115A SER* 6.0 2.9 - - - +
118A GLY 4.4 8.1 - - - +
119A ILE* 1.3 73.9 - - - +
121A VAL* 1.3 61.0 + - - +
122A SER 4.2 0.9 - - - +
129A VAL* 3.9 33.7 - - + +
131A HIS 3.4 7.0 - - - +
132A ARG* 3.7 45.1 - - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.0 9.2 - - + -
67A TYR* 5.9 0.7 - - + -
110A PHE* 3.9 33.2 - - + -
111A ILE 3.6 3.8 - - - +
112A MET* 3.8 16.6 - - + -
119A ILE* 4.6 4.9 - - + +
120A LYS* 1.3 79.6 - - - +
122A SER* 1.3 60.2 + - - +
129A VAL* 4.4 1.6 - - - -
130A LEU* 2.9 24.5 + - - +
131A HIS* 2.8 41.6 + - + -
133A HIS* 4.6 1.1 - - + +
172A TYR* 3.5 29.4 - - + +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE* 3.2 11.1 - - - -
111A ILE* 2.8 52.9 + - - +
120A LYS* 4.2 0.8 - - - +
121A VAL* 1.3 75.1 - - - +
123A THR* 1.3 60.0 + - - +
127A TYR* 3.3 25.1 - - - -
128A ASP 3.3 18.2 - - - -
129A VAL* 3.7 14.1 - - - +
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Residues in contact with THR 123 (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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108A GLU* 5.2 7.4 - - - +
109A GLU 3.9 2.2 - - - -
110A PHE* 3.7 25.8 - - + -
111A ILE 4.4 0.2 - - - -
122A SER* 1.3 77.6 + - - +
124A SER* 1.3 59.7 + - - +
125A ASP* 4.3 2.9 - - - -
126A GLN* 3.5 16.4 + - + +
127A TYR* 3.0 27.5 + - - -
128A ASP* 2.8 37.3 + - + +
130A LEU* 4.9 7.4 - - + -
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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