Contacts of the helix formed by residues 119 - 125 (chain A) in PDB entry 1K3X
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 HIS 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A TYR* 3.4 31.3 - + - -
107A ASP* 5.4 0.9 - - - -
109A GLU* 3.0 39.2 + - - -
111A LEU* 4.0 15.5 - - + -
115A GLN* 3.0 23.7 + - + +
117A THR 3.7 0.4 - - - -
118A THR* 1.3 76.8 + - - +
120A PRO* 1.3 74.3 - - + +
121A PHE* 3.1 31.9 + - + -
122A LEU* 3.4 22.8 + - + +
123A GLN* 2.8 27.0 + - - +
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Residues in contact with PRO 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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118A THR 3.4 5.1 - - - +
119A HIS* 1.3 99.7 - - + +
121A PHE* 1.3 60.1 + - - +
123A GLN* 3.6 7.2 + - + +
124A ARG* 3.2 27.3 + - - +
430C A 5.5 1.3 - - - +
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Residues in contact with PHE 121 (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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50A ARG 4.2 10.1 - - - -
51A GLY* 6.1 0.2 - - - -
52A LYS 5.3 1.3 - - - -
53A ALA* 3.7 25.6 - - + -
65A TYR* 3.4 27.6 - - - +
67A HIS* 4.3 4.9 - + - -
119A HIS* 3.1 10.8 + - + -
120A PRO* 1.3 76.7 - - - +
122A LEU* 1.3 71.3 + - + +
124A ARG* 3.1 26.9 + - + +
125A VAL* 3.1 26.6 + - + +
160A GLN* 4.1 26.5 - - + -
429C A 3.5 36.3 - - - -
430C A 3.3 24.4 + - - +
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Residues in contact with LEU 122 (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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50A ARG* 4.1 29.6 + - + +
53A ALA* 4.2 14.1 - - + -
55A LEU* 4.0 15.5 - - + -
65A TYR* 3.9 18.2 - - + -
111A LEU* 3.7 30.1 - - + -
116A LEU* 3.6 30.9 - - - +
117A THR* 4.6 2.6 - - - +
119A HIS* 3.2 22.5 + - + +
121A PHE* 1.3 80.0 - - + +
123A GLN* 1.3 61.2 + - - +
125A VAL* 3.5 18.7 - - + +
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Residues in contact with GLN 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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117A THR 3.5 21.5 + - - +
118A THR* 4.0 9.4 - - - +
119A HIS 2.8 18.1 + - - +
120A PRO* 4.0 6.5 + - + +
122A LEU* 1.3 78.9 - - - +
124A ARG* 1.3 69.1 + - - +
125A VAL 4.6 2.5 - - - +
514A GOL 4.3 11.4 + - - +
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Residues in contact with ARG 124 (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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120A PRO* 3.2 19.5 + - - +
121A PHE* 3.1 13.6 + - + +
123A GLN* 1.3 88.4 - - - +
125A VAL* 1.3 66.6 + - - +
147A ARG* 5.0 3.1 + - - -
159A ASP* 3.9 10.7 + - - -
160A GLN* 4.0 22.1 - - - +
161A ALA* 3.3 51.6 - - + +
511A GOL 5.4 3.5 + - - +
429C A 4.2 7.1 - - - +
430C A 2.5 41.7 + - - -
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Residues in contact with VAL 125 (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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50A ARG* 4.5 25.4 - - + +
121A PHE* 3.1 36.6 + - + +
122A LEU* 3.5 21.6 - - + +
123A GLN 4.6 2.9 - - - +
124A ARG* 1.3 81.6 - - - +
126A GLY* 1.3 64.2 + - - +
160A GLN* 3.5 11.0 - - + +
164A ALA* 3.3 33.0 - - + -
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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