Contacts of the helix formed by residues 110 - 123 (chain A) in PDB entry 1O5K
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 THR 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PRO* 1.3 77.7 - - - +
111A GLN* 1.3 59.3 + - - +
112A GLU* 3.7 5.7 + - - +
113A GLY* 3.0 17.7 + - - +
114A LEU* 2.9 27.5 + - - +
249B GLU* 3.9 25.1 - - + +
250B THR* 5.0 7.0 - - - +
253B ILE* 3.7 27.7 - - + +
272B PRO 4.9 1.1 + - - -
273B LEU* 5.3 0.2 - - - +
274B VAL* 3.8 15.4 + - + +
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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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109A PRO 4.9 0.4 + - - -
110A THR* 1.3 73.5 - - - +
112A GLU* 1.3 63.9 + - - +
114A LEU* 3.2 18.2 + - - +
115A TYR* 3.0 21.0 + - - +
140A VAL* 4.4 7.1 - - - +
141A ASN 2.9 23.9 + - - -
142A VAL* 3.9 1.6 - - - -
143A LEU* 3.0 37.8 + - + +
146A THR* 2.7 40.3 + - - +
149A ARG* 5.9 0.4 - - - -
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 3.2 7.4 + - - +
111A GLN* 1.3 79.2 - - - +
113A GLY* 1.3 56.5 + - - +
115A TYR* 3.2 8.5 + - - +
116A GLN* 2.8 58.8 + - + +
149A ARG* 2.8 35.5 + - - +
274B VAL* 4.7 14.4 - - + -
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 4.5 2.5 - - - -
110A THR* 3.0 19.6 + - - -
112A GLU* 1.3 74.7 - - - +
114A LEU* 1.3 57.4 + - - +
116A GLN* 3.3 2.3 + - - +
117A HIS* 2.8 31.1 + - - +
272B PRO* 3.2 28.4 - - - +
274B VAL* 4.0 13.4 - - - +
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Residues in contact with LEU 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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103A THR* 3.9 16.4 - - + -
104A PRO* 3.8 20.9 - - + -
109A PRO* 3.7 24.2 - - + +
110A THR 2.9 15.3 + - - +
111A GLN* 3.4 35.7 - - - +
113A GLY* 1.3 73.3 - - - +
115A TYR* 1.3 66.0 + - - +
117A HIS* 3.3 3.1 + - - +
118A TYR* 3.1 40.3 + - + -
140A VAL* 4.1 14.8 - - + -
142A VAL* 4.2 22.7 - - + -
146A THR* 4.7 5.8 - - + -
150A ILE* 4.9 1.3 - - + -
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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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111A GLN 3.0 12.4 + - - +
112A GLU* 3.2 9.6 + - - +
114A LEU* 1.3 78.0 - - - +
116A GLN* 1.3 71.2 + - - +
118A TYR* 3.4 1.9 + - - +
119A LYS* 2.9 62.5 + - + +
146A THR* 4.8 6.3 - - + +
149A ARG* 3.6 54.6 + - + +
150A ILE* 4.0 26.2 - - + -
153A ASP* 2.7 43.0 + - + +
154A LEU* 4.7 4.9 - - + -
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Residues in contact with GLN 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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112A GLU* 2.8 46.7 + - + +
113A GLY* 3.8 2.0 - - - +
115A TYR* 1.3 81.5 - - + +
117A HIS* 1.3 56.6 + - - +
119A LYS* 2.4 37.7 + - - +
120A TYR* 2.9 31.2 + - - +
271B LEU* 3.7 29.5 - - + +
274B VAL* 4.7 5.6 - - + -
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Residues in contact with HIS 117 (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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78A THR 4.0 3.7 + - - -
81A THR* 2.7 44.9 + - - +
84A THR* 3.6 23.5 + - - -
101A VAL* 4.1 10.5 - - - +
102A VAL 4.3 0.2 + - - -
104A PRO* 3.6 39.7 - - + +
113A GLY 2.8 17.1 + - - +
114A LEU* 3.5 7.0 - - - +
115A TYR 3.3 0.2 - - - -
116A GLN* 1.3 76.9 - - - +
118A TYR* 1.3 79.3 + + - +
120A TYR* 3.4 2.9 + - - +
121A ILE* 3.2 42.8 + - + +
271B LEU* 4.7 1.7 - - - +
272B PRO* 4.2 6.3 - - + +
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Residues in contact with TYR 118 (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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101A VAL* 2.7 48.4 + - + -
102A VAL 3.3 0.9 - - - -
103A THR* 3.1 21.7 + - + -
114A LEU* 3.1 40.3 + - + +
115A TYR 4.0 1.1 - - - +
117A HIS* 1.3 87.3 - + - +
119A LYS* 1.3 59.8 + - - +
121A ILE* 3.4 6.9 + - + +
122A SER* 2.8 33.1 + - - -
129A ILE* 4.5 13.5 - - + +
131A VAL* 3.7 38.1 - - + +
142A VAL* 5.5 1.3 - - + -
150A ILE* 3.9 17.9 - - + -
154A LEU* 3.8 15.9 - - + -
157A VAL* 4.7 5.6 - - + +
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Residues in contact with LYS 119 (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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115A TYR* 2.9 43.5 + - + +
116A GLN* 2.4 49.9 + - - +
118A TYR* 1.3 73.8 - - - +
120A TYR* 1.3 66.8 + - - +
122A SER* 3.3 0.9 + - - -
123A GLU* 2.9 58.3 + - - +
154A LEU* 3.6 25.7 - - + +
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Residues in contact with TYR 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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81A THR* 3.5 31.4 - - + -
82A GLU* 4.9 10.0 - - + +
85A LEU* 3.6 30.0 - - + +
116A GLN 2.9 18.5 + - - +
117A HIS 3.6 4.3 - - - +
118A TYR 3.4 0.2 - - - -
119A LYS* 1.3 77.3 - - - +
121A ILE* 1.3 64.8 + - + +
123A GLU* 3.6 4.7 + - - -
124A ARG* 3.1 66.7 + - - +
271B LEU* 4.5 13.9 - - + -
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Residues in contact with ILE 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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81A THR* 4.5 13.9 - - + +
84A THR* 3.5 28.9 - - + -
85A LEU* 4.3 14.9 - - + +
88A VAL* 4.1 29.8 - - + -
101A VAL* 4.4 8.1 - - + -
117A HIS* 3.2 40.9 + - + +
118A TYR* 3.8 7.9 - - + +
119A LYS 3.2 0.6 - - - -
120A TYR* 1.3 76.8 - - + +
122A SER* 1.3 65.5 + - - +
124A ARG* 2.9 14.6 + - - +
125A THR* 3.3 12.5 + - - +
129A ILE* 4.1 15.9 - - + -
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Residues in contact with SER 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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118A TYR 2.8 22.3 + - - -
119A LYS* 3.7 4.5 - - - -
121A ILE* 1.3 74.0 - - - +
123A GLU* 1.3 60.2 + - - +
124A ARG 3.1 4.2 + - - -
125A THR 3.3 16.5 - - - +
129A ILE* 3.7 20.2 - - - +
154A LEU* 3.7 29.5 - - - +
155A LYS 4.5 0.5 + - - -
156A ASN* 3.3 22.3 + - - +
157A VAL* 4.3 2.5 - - - -
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Residues in contact with GLU 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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119A LYS* 2.9 57.8 + - + +
120A TYR* 4.5 1.0 - - - -
121A ILE 3.2 0.2 - - - -
122A SER* 1.3 77.0 - - - +
124A ARG* 1.3 86.1 + - + +
125A THR 3.8 0.9 - - - -
154A LEU* 5.6 2.2 - - + +
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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