Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 2KK0
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A HIS* 4.9 13.4 + - - +
101A ILE* 4.3 3.9 - - - +
102A THR* 1.3 82.4 - - - +
104A ALA* 1.3 53.5 + - - +
105A ALA 3.3 2.5 - - - -
106A PHE* 3.1 21.2 + - - +
107A THR* 2.8 47.3 + - - -
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Residues in contact with ALA 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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59A MET* 4.6 8.7 - - + -
92A THR* 3.9 21.5 - - + -
98A PRO 5.0 2.0 - - - +
99A THR* 5.5 2.7 - - - +
101A ILE* 3.6 40.0 + - + +
102A THR 3.4 3.6 + - - -
103A SER* 1.3 76.3 - - - +
105A ALA* 1.3 63.9 + - - +
107A THR* 3.7 5.3 - - - -
108A LEU* 2.9 33.3 + - + +
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Residues in contact with ALA 105 (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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86A LYS* 5.9 0.9 - - - +
88A TRP* 3.5 40.9 - - + -
92A THR* 5.0 1.7 - - - +
102A THR 5.2 1.0 + - - +
103A SER 3.3 0.6 - - - -
104A ALA* 1.3 77.9 - - - +
106A PHE* 1.3 57.4 + - - +
108A LEU* 4.1 1.1 - - - +
109A ARG* 3.1 40.4 + - - +
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Residues in contact with PHE 106 (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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103A SER* 3.1 22.8 + - - +
105A ALA* 1.3 76.8 - - - +
107A THR* 1.3 63.6 + - - +
109A ARG* 3.4 30.8 + - + +
110A THR* 2.9 48.1 + - - -
136A ILE* 5.4 11.7 - - + -
140A ARG* 5.7 9.9 - - + -
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Residues in contact with THR 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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7A HIS* 5.8 2.6 - - - -
57A PRO* 5.8 2.7 - - + -
59A MET* 3.8 25.6 - - + +
103A SER* 2.8 36.4 + - - -
104A ALA 3.7 2.7 - - - -
106A PHE* 1.3 73.5 - - - +
108A LEU* 1.3 60.2 + - + +
110A THR* 3.2 6.1 + - - -
111A GLN* 2.9 51.3 + - + +
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Residues in contact with LEU 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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59A MET* 4.4 18.2 - - + -
64A LEU* 3.5 37.9 - - + -
69A LEU* 4.8 6.2 - - + +
88A TRP* 3.7 21.1 - - + -
91A ILE* 4.3 20.2 - - + -
92A THR* 3.4 35.7 - - + +
95A LEU* 5.0 0.2 - - + -
97A LEU* 4.4 8.1 - - + -
104A ALA 2.9 18.6 + - - +
105A ALA* 5.1 0.4 - - - +
107A THR* 1.3 75.5 - - + +
109A ARG* 1.3 58.1 + - - +
111A GLN* 4.6 3.1 - - - +
112A TYR* 2.8 35.9 + - - +
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Residues in contact with ARG 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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79A LEU* 4.3 3.0 - - + +
83A ILE* 3.8 32.4 - - + +
86A LYS* 4.7 9.3 - - - +
88A TRP* 3.2 49.1 - - + +
105A ALA* 3.1 27.1 + - - +
106A PHE* 3.4 32.5 - - + +
108A LEU* 1.3 77.4 - - - +
110A THR* 1.3 61.1 + - - +
113A MET* 3.2 30.5 + - + +
136A ILE* 4.9 10.6 - - - +
139A ASN* 3.0 40.0 + - - +
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Residues in contact with THR 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 PHE* 2.9 35.4 + - - -
107A THR* 3.5 10.0 - - - -
108A LEU 3.2 0.2 - - - -
109A ARG* 1.3 75.2 - - - +
111A GLN* 1.3 75.2 + - - +
113A MET* 3.3 10.6 + - - +
114A LYS* 3.1 45.6 + - + +
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Residues in contact with GLN 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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55A ARG* 5.2 1.7 + - - -
57A PRO* 3.6 41.8 - - + +
64A LEU* 4.0 14.6 - - + -
66A LEU* 6.4 1.3 - - + -
107A THR* 2.9 34.5 + - + +
108A LEU 4.1 0.9 - - - +
110A THR* 1.3 85.8 - - - +
112A TYR* 1.3 63.7 + - - +
114A LYS* 3.2 17.8 + - - +
115A TYR* 3.0 45.6 + - + +
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Residues in contact with TYR 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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66A LEU* 6.6 0.2 - - - -
69A LEU* 3.6 29.0 - - + +
70A TYR* 3.7 29.6 - - - -
73A VAL* 3.4 34.2 - - + +
74A THR* 3.9 5.9 - - - +
79A LEU* 3.5 32.5 - - + -
88A TRP* 4.7 4.3 - + + -
108A LEU 2.8 24.4 + - - +
109A ARG 4.3 2.0 - - - +
111A GLN* 1.3 71.2 - - - +
113A MET* 1.3 58.6 + - - +
116A LEU* 2.6 77.6 + - + +
117A TYR* 4.9 0.2 - - - -
120A GLU* 2.9 26.7 + - - -
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Residues in contact with MET 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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79A LEU* 3.8 14.4 - - + -
109A ARG* 3.2 28.5 + - + +
110A THR* 3.3 9.5 + - - +
112A TYR* 1.3 79.5 - - - +
114A LYS* 1.3 64.4 + - + +
117A TYR* 3.5 20.6 - - + +
118A PRO* 4.8 1.4 - - - +
132A LEU* 3.9 33.2 - - + -
136A ILE* 3.4 33.0 - - + -
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Residues in contact with LYS 114 (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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46A MET* 4.8 0.7 - - - +
51A THR* 3.8 20.8 + - - +
55A ARG* 4.1 16.1 - - - +
110A THR* 3.1 34.5 + - + +
111A GLN* 3.5 27.7 + - - +
112A TYR 3.1 0.2 - - - -
113A MET* 1.3 80.3 - - + +
115A TYR* 1.3 75.7 + - + +
118A PRO* 5.0 4.2 - - - +
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Residues in contact with TYR 115 (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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42A LEU* 4.5 7.4 - - + +
46A MET* 3.7 36.5 - - + +
52A PRO 3.9 4.7 - - - -
53A VAL* 3.8 30.5 - - + -
54A ASN* 2.7 16.2 + - - -
55A ARG* 2.7 40.3 + - - -
56A ILE* 5.7 0.4 - - + -
57A PRO* 4.3 10.9 - - + +
66A LEU* 4.8 18.2 - - + -
111A GLN* 3.0 42.3 + - + +
114A LYS* 1.3 91.6 - - + +
116A LEU* 1.3 72.6 + - + +
117A TYR 3.6 4.9 + - - -
118A PRO* 4.2 8.7 - - - +
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Residues in contact with LEU 116 (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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38A PHE* 4.4 2.9 - - + -
42A LEU* 3.4 37.7 - - + -
66A LEU* 3.1 50.3 - - + +
69A LEU* 3.9 12.6 - - + -
70A TYR* 3.9 25.4 - - + +
112A TYR* 2.6 74.6 + - + +
115A TYR* 1.3 72.0 - - + +
117A TYR* 1.3 57.5 + - - +
119A TYR* 5.9 0.2 - - - -
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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