Contacts of the helix formed by residues 113 - 125 (chain O) in PDB entry 1KD1
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 SER 113 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3036B C 4.9 0.4 + - - -
3047B A 3.4 11.8 + - - -
3048B C 3.3 13.0 - - - -
78O MET* 4.0 0.4 - - - -
108O SER 4.1 4.3 + - - -
110O THR* 2.5 43.2 + - - +
111O PRO 3.1 1.0 - - - -
112O GLY* 1.3 82.4 - - - +
114O LYS* 1.3 67.6 + - - +
115O VAL* 3.2 18.4 - - - -
116O PHE* 3.1 8.0 + - - +
117O ALA* 3.1 17.5 + - - +
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Residues in contact with LYS 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3048B C 2.5 42.0 + - - +
3049B G 3.4 20.7 + - - +
38O LYS* 3.8 22.7 - - + +
39O SER 4.7 10.3 + - - -
40O ASN 5.4 1.6 + - - -
43O VAL* 4.5 12.8 - - + +
76O GLY* 3.4 22.0 + - - +
77O ASN 4.0 15.0 - - - +
78O MET* 3.7 24.4 - - + -
81O ALA* 3.7 10.4 - - + +
113O SER* 1.3 72.7 - - - +
115O VAL* 1.3 57.9 + - - +
117O ALA* 2.9 4.8 + - - +
118O ILE* 2.8 32.8 + - - +
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Residues in contact with VAL 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3048B C 4.6 0.4 + - - -
36O ALA* 3.9 33.7 - - + +
38O LYS* 4.6 13.6 - - + +
102O LEU* 4.4 2.3 - - - +
104O ILE* 4.2 23.8 - - + -
107O ASN* 4.3 23.3 - - + +
108O SER 4.5 12.1 - - - +
113O SER* 4.1 15.7 - - - -
114O LYS* 1.3 76.2 - - - +
116O PHE* 1.3 70.9 + - + +
118O ILE* 3.0 14.3 + - + +
119O GLN* 2.8 24.8 + - - +
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Residues in contact with PHE 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2413A A 3.7 46.0 - + - -
102O LEU* 3.8 12.3 - - + -
104O ILE* 5.3 1.1 - - + -
109O PRO* 3.5 26.9 - - + -
110O THR 3.3 26.9 - - - -
112O GLY 5.0 0.2 - - - -
113O SER* 3.1 11.8 + - - +
115O VAL* 1.3 80.0 - - + +
117O ALA* 1.3 60.9 + - - +
119O GLN* 3.2 21.3 + - - +
120O GLU* 2.9 28.5 + - - +
135O VAL* 3.4 35.4 - - + +
136O LEU* 3.8 19.3 - - + +
137O ALA 6.2 0.2 - - - -
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Residues in contact with ALA 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O MET* 4.0 24.0 - - + +
81O ALA* 4.0 10.5 - - + -
82O TYR* 3.5 20.7 - - + +
113O SER 3.1 10.8 + - - +
114O LYS* 2.9 15.4 + - - +
116O PHE* 1.3 74.4 - - - +
118O ILE* 1.3 66.7 + - - +
120O GLU* 3.1 11.6 + - - +
121O GLY 3.0 18.9 + - - -
136O LEU* 6.4 0.2 - - - -
137O ALA 6.3 1.3 - - - +
142O THR* 5.1 4.5 - - + +
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Residues in contact with ILE 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O LEU* 4.9 10.5 - - + -
36O ALA* 3.9 24.5 - - + -
37O ARG 4.3 4.9 - - - +
38O LYS* 5.4 0.7 - - + -
43O VAL* 3.3 31.9 - - + -
44O ARG 3.7 14.6 - - - +
45O ALA* 3.7 23.6 - - + -
81O ALA* 3.8 22.2 - - + +
85O GLY* 3.6 8.5 - - - -
114O LYS 2.8 18.1 + - - +
115O VAL* 3.0 14.3 + - + +
117O ALA* 1.3 76.2 - - - +
119O GLN* 1.3 60.8 + - - +
121O GLY 3.2 1.2 + - - -
122O ALA* 3.1 21.3 + - - +
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Residues in contact with GLN 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2413A A 5.0 4.9 + - - +
34O LEU* 4.2 11.4 - - + -
102O LEU* 3.7 35.5 - - + +
115O VAL 2.8 12.2 + - - +
116O PHE* 3.5 19.7 - - - +
117O ALA 3.2 0.2 - - - -
118O ILE* 1.3 77.3 - - - +
120O GLU* 1.3 59.4 + - - +
122O ALA* 4.0 1.4 - - - +
123O ILE* 2.8 42.4 + - + +
129O ILE* 3.5 19.6 - - + +
130O PRO 3.4 23.4 + - - -
131O HIS* 3.5 20.4 - - - +
132O ASN 5.0 0.2 + - - -
135O VAL* 5.2 0.5 - - - +
136O LEU* 4.0 10.2 - - + +
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Residues in contact with GLU 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TYR* 4.1 12.7 - - + -
116O PHE 2.9 16.5 + - - +
117O ALA* 3.1 9.5 + - - +
119O GLN* 1.3 73.2 - - - +
121O GLY* 1.3 66.4 + - - +
123O ILE* 3.3 11.8 + - + +
124O ASP* 3.0 38.5 + - - +
136O LEU* 3.7 38.8 - - + +
137O ALA* 4.1 11.3 + - - +
139O TRP* 4.1 19.8 + - - +
142O THR* 4.1 11.4 + - - +
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Residues in contact with GLY 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TYR* 3.5 39.9 - - - -
86O LEU* 3.4 16.7 - - - +
117O ALA 3.0 9.9 + - - -
118O ILE 3.7 1.1 - - - -
120O GLU* 1.3 77.0 - - - +
122O ALA* 1.3 63.8 + - - +
124O ASP* 3.1 4.0 + - - +
125O ALA 3.0 17.8 + - - -
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Residues in contact with ALA 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O LEU* 3.7 37.5 - - + -
85O GLY* 3.4 20.1 - - - +
89O GLY* 4.1 10.1 - - - -
118O ILE 3.1 11.9 + - - +
119O GLN 4.0 1.3 - - - +
121O GLY* 1.3 74.2 - - - +
123O ILE* 1.3 62.1 + - - +
125O ALA* 3.1 15.9 + - - +
127O LEU* 3.3 20.1 + - + +
129O ILE* 4.0 5.6 - - + -
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Residues in contact with ILE 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119O GLN* 2.8 45.2 + - + +
120O GLU* 3.5 10.1 - - + +
121O GLY 3.2 0.2 - - - -
122O ALA* 1.3 72.5 - - - +
124O ASP* 1.3 67.0 + - - +
126O GLY* 2.8 19.8 + - - -
127O LEU 3.2 22.0 - - - +
128O ASP* 5.8 0.2 - - - -
129O ILE* 4.2 15.0 - - + +
131O HIS* 3.8 40.6 - - + +
136O LEU* 5.8 3.6 - - + -
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Residues in contact with ASP 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TYR* 2.5 35.2 + - - +
86O LEU* 4.1 5.9 - - + +
120O GLU* 3.0 25.9 + - - +
121O GLY 3.6 4.9 - - - +
123O ILE* 1.3 76.2 - - - +
125O ALA* 1.3 61.9 + - - +
126O GLY* 2.9 7.5 + - - -
139O TRP* 5.4 0.2 - - - -
176O ARG* 4.0 14.7 + - - +
180O LEU* 5.3 6.0 - - + +
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Residues in contact with ALA 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O LEU* 3.3 28.9 - - + +
89O GLY* 3.4 6.7 - - - -
90O LEU* 3.4 42.6 - - + +
93O GLN* 3.8 12.4 - - - +
121O GLY 3.0 8.2 + - - +
122O ALA 3.2 13.2 - - - +
123O ILE 3.1 0.4 - - - -
124O ASP* 1.3 75.5 - - - +
126O GLY* 1.3 57.4 + - - +
127O LEU 3.7 0.2 - - - -
180O LEU* 5.8 0.4 - - - -
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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