Contacts of the helix formed by residues 95 - 113 (chain A) in PDB entry 1K0Y
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 PRO 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL 3.3 3.6 - - - +
94A ASP* 1.3 94.1 - - - +
96A VAL* 1.4 61.3 + - - +
98A PHE* 3.2 30.3 + - + +
99A LYS* 4.2 4.2 + - - +
137A THR* 4.3 8.9 - - + +
140A TYR* 4.1 12.6 - - + -
637D TRP* 3.8 16.8 - - + +
802D CNO 3.4 45.1 - - + +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 2.9 19.9 + - - +
95A PRO* 1.4 76.2 - - - +
97A ASN* 1.4 77.7 + - - +
99A LYS* 3.1 30.8 + - + +
100A LEU* 3.6 5.6 + - - +
701D GLU* 3.9 24.2 - - + +
801D CNO 3.4 55.6 - - + +
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 4.8 1.2 - - - +
38A THR* 4.8 2.4 + - - -
39A THR* 3.6 22.3 + - + +
42A TYR* 3.5 20.9 + - - -
93A VAL* 3.7 12.6 - - + -
94A ASP* 3.0 26.9 + - - +
96A VAL* 1.4 81.9 - - - +
98A PHE* 1.4 61.5 + - - +
100A LEU* 3.2 15.5 + - - +
101A LEU* 3.1 19.1 + - - +
143A HEM 3.3 19.0 - - + +
699D ASP* 2.9 29.8 + - - +
801D CNO 5.0 0.7 - - - +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.0 18.2 - + + -
93A VAL* 3.9 17.9 - - + -
94A ASP 4.0 1.3 - - - -
95A PRO* 3.2 19.3 + - + +
97A ASN* 1.4 77.0 - - - +
99A LYS* 1.4 53.9 + - + +
101A LEU* 3.5 2.1 + - - +
102A SER* 2.8 37.7 + - - -
133A SER* 3.5 32.5 + - - +
136A LEU* 4.0 18.2 - - + -
137A THR* 3.5 26.0 - - + -
140A TYR* 3.6 20.9 - - - -
143A HEM 3.4 49.7 - + + +
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Residues in contact with LYS 99 (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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95A PRO 5.1 3.1 - - - +
96A VAL* 3.1 23.1 + - + +
98A PHE* 1.4 78.4 - - + +
100A LEU* 1.4 59.9 + - + +
102A SER* 3.5 6.1 + - - -
103A HIS* 3.0 29.6 + - - +
130A ALA* 6.0 1.2 - - - +
133A SER* 5.6 1.3 - - - -
499C LYS* 6.4 1.6 - - - +
801D CNO 3.4 84.2 + - + +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 4.6 2.0 - - + -
36A PHE* 3.8 41.8 - - + -
39A THR* 3.8 27.4 - - + -
96A VAL 3.8 10.8 - - - +
97A ASN* 3.2 16.0 + - - +
99A LYS* 1.4 74.1 - - - +
101A LEU* 1.4 64.7 + - - +
103A HIS* 3.4 6.0 + - - +
104A CYS* 3.2 28.3 + - - -
801D CNO 3.7 62.1 - - + +
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Residues in contact with LEU 101 (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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28A ALA* 4.4 15.0 - - + +
29A LEU* 4.1 22.2 - - + -
32A MET* 3.7 27.7 - - + -
62A VAL* 4.7 9.9 - - + -
97A ASN 3.1 13.9 + - - +
98A PHE* 4.1 2.9 - - - +
100A LEU* 1.4 75.3 - - - +
102A SER* 1.4 52.2 + - - +
104A CYS* 3.2 2.2 + - - +
105A LEU* 2.8 52.1 + - + +
143A HEM 3.5 55.6 - - + -
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Residues in contact with SER 102 (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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98A PHE 2.8 24.4 + - - -
99A LYS* 3.7 7.9 - - - -
101A LEU* 1.4 72.2 - - - +
103A HIS* 1.4 60.0 + - - +
105A LEU* 3.3 4.2 + - - -
106A LEU* 2.9 27.3 + - - +
126A ASP* 5.5 5.2 - - - -
129A LEU* 3.4 41.7 + - - +
130A ALA* 5.4 0.4 - - - -
133A SER* 3.4 15.9 + - - -
143A HEM 5.2 6.2 - - - +
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.1 20.4 - + - -
99A LYS 3.0 18.8 + - - +
100A LEU* 3.7 4.3 - - - +
101A LEU 3.3 0.2 - - - -
102A SER* 1.4 75.7 - - - +
104A CYS* 1.4 59.0 + - - +
106A LEU* 3.3 10.9 + - - +
107A VAL* 2.9 47.5 + - + +
126A ASP* 6.0 0.2 - - - -
308B ASN* 3.6 44.9 + - + +
311B VAL* 4.3 2.7 - - + -
312B CYS* 4.3 6.7 - - - -
327B GLN* 4.1 4.9 - - - -
331B GLN* 2.8 29.9 + - - -
801D CNO 3.9 18.3 - + + -
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Residues in contact with CYS 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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28A ALA* 3.4 21.8 - - - +
31A ARG* 3.9 9.1 - - + -
32A MET* 3.5 32.5 - - + +
36A PHE* 3.8 18.6 - - - -
100A LEU 3.2 15.9 + - - +
101A LEU 3.2 6.3 + - - +
103A HIS* 1.4 76.0 - - - +
105A LEU* 1.4 60.4 + - - +
107A VAL* 3.5 7.6 + - - +
108A THR* 2.8 32.3 + - - -
327B GLN* 4.0 12.6 - - - +
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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
----------------------------------------------------------
14A TRP* 5.6 5.2 - - + -
24A TYR* 4.6 9.0 - - + +
25A GLY* 4.9 8.1 - - - -
28A ALA* 3.5 18.2 - - + -
62A VAL* 4.9 6.1 - - + -
66A LEU* 4.3 26.5 - - + -
101A LEU* 2.8 51.0 + - + +
102A SER* 3.5 9.4 - - - +
104A CYS* 1.4 74.7 - - - +
106A LEU* 1.4 58.5 + - - +
108A THR* 3.2 4.9 + - + -
109A LEU* 2.9 44.0 + - + +
129A LEU* 4.1 15.5 - - + -
143A HEM 5.0 4.9 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER 2.9 13.0 + - - +
103A HIS* 3.4 14.8 - - - +
105A LEU* 1.4 75.8 - - - +
107A VAL* 1.4 56.0 + - - +
109A LEU* 3.4 6.6 + - + +
110A ALA* 2.9 29.5 + - - +
117A PHE* 4.1 21.8 - - + -
122A HIS* 4.0 22.2 - - + +
125A LEU* 3.7 31.9 - - + -
126A ASP* 3.5 30.7 - - - +
129A LEU* 4.0 13.9 - - + +
235B TYR* 5.1 2.9 - - - +
312B CYS* 4.3 13.2 - - - -
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Residues in contact with VAL 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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31A ARG* 3.9 13.9 - - - +
103A HIS* 2.9 48.0 + - + +
104A CYS 3.8 5.2 - - - +
106A LEU* 1.4 74.0 - - - +
108A THR* 1.4 62.2 + - - +
110A ALA* 3.3 8.1 + - - +
111A ALA* 3.0 22.9 + - - +
311B VAL* 3.8 12.3 - - + -
312B CYS* 4.1 9.2 - - - -
315B ALA* 3.7 18.3 - - + +
322B PHE* 4.1 5.2 - - + -
327B GLN* 3.5 28.3 - - - +
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Residues in contact with THR 108 (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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24A TYR* 3.4 39.9 - - + +
27A GLU* 3.7 26.5 - - - -
28A ALA* 3.3 17.8 + - - -
31A ARG* 3.3 12.8 - - - +
104A CYS 2.8 19.3 + - - -
105A LEU* 3.2 9.6 + - - -
107A VAL* 1.4 75.3 - - - +
109A LEU* 1.4 61.9 + - + +
111A ALA* 3.3 2.4 + - - +
112A HIS* 3.1 33.4 + - + -
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Residues in contact with LEU 109 (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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13A ALA* 6.2 0.7 - - + -
14A TRP* 4.5 18.8 - - + -
17A VAL* 3.6 30.7 - - + -
24A TYR* 4.2 16.4 - - + -
105A LEU* 2.9 33.1 + - + +
106A LEU* 3.8 9.6 - - + +
108A THR* 1.4 71.8 - - + +
110A ALA* 1.4 56.7 + - - +
112A HIS* 3.1 2.9 + - - +
113A LEU* 2.7 53.4 + - + +
117A PHE* 4.5 2.0 - - + -
125A LEU* 4.0 34.8 - - + -
129A LEU* 5.5 4.5 - - + -
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Residues in contact with ALA 110 (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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106A LEU 2.9 14.6 + - - +
107A VAL* 3.5 10.5 - - - +
109A LEU* 1.4 77.0 - - - +
111A ALA* 1.4 60.0 + - - +
112A HIS 3.4 0.9 + - - -
113A LEU 3.6 5.5 + - - -
114A PRO* 4.3 0.9 - - - +
117A PHE* 3.7 32.1 - - + -
312B CYS* 3.7 24.5 - - - +
315B ALA* 4.1 2.0 - - + -
316B HIS* 3.4 30.0 - - - +
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Residues in contact with ALA 111 (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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31A ARG* 4.3 17.3 - - - +
107A VAL 3.0 16.2 + - - +
108A THR 3.7 5.8 - - - +
109A LEU 3.3 0.2 - - - -
110A ALA* 1.4 75.0 - - - +
112A HIS* 1.4 67.3 + - + +
114A PRO* 4.8 3.7 - - - +
315B ALA* 3.5 20.8 + - + +
319B GLY* 3.5 35.6 - - - +
320B LYS* 4.3 2.9 + - - +
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Residues in contact with HIS 112 (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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16A LYS* 5.1 3.5 + - - -
23A GLU* 4.8 6.7 - - - -
24A TYR* 3.4 54.1 + + + +
27A GLU* 2.8 34.6 + - - -
108A THR* 3.1 28.1 + - + +
109A LEU 3.1 3.8 + - - +
111A ALA* 1.4 84.4 + - + +
113A LEU* 1.4 63.0 + - + +
114A PRO* 3.2 13.7 - - - +
320B LYS* 6.1 4.5 - - + -
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Residues in contact with LEU 113 (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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13A ALA* 4.1 31.0 - - + +
16A LYS* 4.3 26.5 - - + +
17A VAL* 4.8 10.3 - - + +
24A TYR* 5.1 3.6 - - + +
109A LEU* 2.7 46.0 + - + +
110A ALA 3.6 5.1 + - - -
112A HIS* 1.4 83.2 - - + +
114A PRO* 1.3 67.0 - - - +
115A ALA 3.3 2.7 - - - -
116A GLU* 3.6 26.5 - - + +
117A PHE* 3.1 27.7 + - + +
121A VAL* 6.0 0.2 - - + -
125A LEU* 5.2 4.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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