Contacts of the helix formed by residues 140 - 155 (chain C) in PDB entry 1KPS
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 ASN 140 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ILE* 3.0 22.2 + - + +
138C CYS 3.3 2.4 + - - -
139C GLN* 1.3 83.4 + - + +
141C ARG* 1.3 69.1 + - - +
142C VAL* 3.1 11.0 - - - +
143C GLU* 2.9 42.7 + - + +
144C TYR 3.0 4.9 + - - -
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Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B CYS 4.2 5.3 + - - -
577B PHE* 3.2 56.0 - - + +
136C ILE 3.7 0.4 + - - -
137C TYR* 2.7 78.6 + - - -
138C CYS* 4.3 1.2 + - - +
140C ASN* 1.3 71.8 - - - +
142C VAL* 1.3 65.0 + - + +
144C TYR* 3.0 13.2 + - - +
145C GLU* 2.8 41.7 + - + +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ASN* 3.0 10.0 + - - +
141C ARG* 1.3 78.2 - - + +
143C GLU* 1.3 67.6 + - + +
145C GLU* 3.0 21.5 + - - +
146C LYS* 3.0 23.9 + - + +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ILE* 3.8 18.2 - - + -
140C ASN* 2.9 33.4 + - + +
142C VAL* 1.3 79.8 - - - +
144C TYR* 1.3 66.3 + - - +
146C LYS* 3.2 35.3 + - - +
147C ARG* 3.0 40.2 + - - +
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TRP* 4.4 8.1 - + - -
82C PHE* 3.7 32.0 + + - -
83C HIS* 4.4 10.9 - - - -
84C PRO* 3.4 32.2 - - + +
120C LEU 4.5 1.6 + - - -
121C ASN* 6.2 1.3 - - - -
123C PRO* 4.4 7.9 - - + +
133C ALA 4.1 1.3 - - - -
136C ILE* 3.4 15.3 - - - +
137C TYR* 3.7 48.7 - + + -
140C ASN 3.0 9.3 + - - +
141C ARG* 3.0 17.2 + - - +
143C GLU* 1.3 76.5 - - - +
145C GLU* 1.3 69.1 + - + +
147C ARG* 3.3 1.4 + - - +
148C VAL* 2.8 46.8 + - + +
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PRO* 6.2 2.7 - - + -
141C ARG* 2.8 37.2 + - + +
142C VAL* 3.0 36.1 + - - +
144C TYR* 1.3 78.2 - - + +
146C LYS* 1.3 65.1 + - - +
148C VAL* 3.0 17.8 + - - +
149C ARG* 3.1 19.2 + - + +
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.0 11.8 + - + +
143C GLU* 3.4 36.7 + - - +
145C GLU* 1.3 80.7 - - - +
147C ARG* 1.3 69.7 + - + +
149C ARG* 3.2 6.4 + - - +
150C ALA* 3.0 22.9 + - + +
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Residues in contact with ARG 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PHE* 2.9 49.2 - - + +
132C GLU* 3.3 26.8 + - - -
136C ILE* 4.0 21.8 - - - +
143C GLU* 3.0 36.6 + - - +
146C LYS* 1.3 81.6 - - + +
148C VAL* 1.3 63.3 + - - +
150C ALA* 3.8 8.4 - - + +
151C GLN* 2.9 25.7 + - - +
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PRO* 4.3 15.0 - - + +
53C TRP* 3.3 48.1 - - + +
82C PHE* 4.2 5.6 - - + -
144C TYR* 2.8 63.8 + - + +
145C GLU* 3.0 8.7 + - - +
147C ARG* 1.3 74.7 - - - +
149C ARG* 1.3 58.4 + - - +
151C GLN* 3.2 12.8 + - - +
152C ALA* 2.9 23.9 + - - +
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLY 5.7 0.8 + - - -
51C THR 5.0 1.6 + - - -
52C PRO* 3.4 46.7 + - + +
54C GLU* 5.7 5.5 + - - +
145C GLU* 3.1 15.7 + - + +
146C LYS* 3.8 6.5 - - - +
148C VAL* 1.3 72.1 - - - +
150C ALA* 1.3 56.4 + - - +
151C GLN 3.0 1.8 - - - -
152C ALA* 2.8 9.1 + - - +
153C LYS* 2.6 38.0 + - - +
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 3.0 19.8 + - + +
147C ARG* 3.8 8.5 - - + +
149C ARG* 1.3 76.9 - - - +
151C GLN* 1.3 56.9 + - - +
153C LYS* 3.5 8.1 + - - +
154C LYS* 3.0 28.4 + - - +
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TRP* 4.0 18.7 - - + -
58C PHE* 3.9 3.9 - - + -
80C PRO 4.7 0.2 - - - +
81C LEU* 3.2 23.0 - - + +
82C PHE* 2.5 61.3 + - + +
147C ARG* 2.9 17.1 + - - +
148C VAL* 3.3 6.3 + - - +
150C ALA* 1.3 80.4 - - - +
152C ALA* 1.3 56.3 + - - +
154C LYS* 3.8 5.8 - - + -
155C PHE* 3.1 50.5 + - + +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PRO 3.4 25.6 - - - +
53C TRP* 4.1 19.3 - - + +
54C GLU 4.6 5.4 - - - +
56C GLY* 3.7 8.0 + - - -
58C PHE* 4.0 12.3 - - + -
148C VAL* 2.9 9.5 + - + +
149C ARG* 2.8 8.8 + - - +
151C GLN* 1.3 76.7 - - - +
153C LYS* 1.3 63.1 + - - +
154C LYS 3.2 0.4 - - - -
156C ALA* 3.4 21.0 + - - +
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ARG 2.6 19.4 + - - +
150C ALA* 3.9 8.3 - - - +
152C ALA* 1.3 72.8 - - - +
154C LYS* 1.3 65.0 + - - +
156C ALA* 3.4 18.4 + - - +
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ALA 3.0 19.1 + - - +
151C GLN* 3.7 8.3 - - + +
153C LYS* 1.3 79.4 - - - +
155C PHE* 1.3 81.0 + - + +
156C ALA 2.9 11.1 + - - +
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Residues in contact with PHE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLY* 4.0 2.5 - - - -
57C LEU* 2.5 48.6 + - - +
58C PHE* 3.6 32.8 - + + -
59C LYS 5.3 2.7 - - - -
78C GLU 4.9 1.3 - - - -
79C PRO* 3.4 44.6 - - + -
80C PRO 5.1 2.9 - - - -
81C LEU* 3.8 18.4 - - + -
151C GLN* 3.1 31.5 + - + -
152C ALA 3.9 0.2 + - - -
153C LYS 3.5 0.2 - - - -
154C LYS* 1.3 100.3 - - + +
156C ALA* 1.3 54.9 + - - +
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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