Contacts of the helix formed by residues 109 - 127 (chain A) in PDB entry 4KBQ
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 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLN* 2.8 26.3 + - - +
107A MET* 3.8 5.9 + - - +
108A GLU* 1.3 75.1 - - - +
110A TYR* 1.3 62.8 + - - +
111A ASP 3.4 2.0 - - - -
112A GLU* 3.2 23.8 - - - +
113A ALA* 3.3 17.3 + - - +
38B VAL* 4.7 9.4 + - - +
40B ARG* 3.8 16.3 + - - +
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.0 22.4 - - + -
108A GLU* 3.1 54.9 + - + +
109A SER* 1.3 70.8 - - - +
111A ASP* 1.3 64.5 + - - +
113A ALA* 3.3 6.6 + - - +
114A ILE* 3.0 29.9 + - - +
142A ALA 4.9 1.6 - - - +
145A LYS* 4.0 22.9 + - + +
146A ARG* 3.7 38.1 - - + -
149A SER* 3.3 37.1 + - - -
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER 3.4 1.0 + - - -
110A TYR* 1.3 79.2 - - - +
112A GLU* 1.3 71.7 + - - +
114A ILE* 3.6 6.6 + - - +
115A ALA* 3.3 18.9 + - - +
146A ARG* 3.7 29.2 + - - +
641D THR* 4.0 7.9 - - + +
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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
----------------------------------------------------------
104A GLN* 3.1 24.1 - - + +
109A SER* 3.2 28.2 - - - +
111A ASP* 1.3 77.4 + - - +
113A ALA* 1.3 60.9 + - - +
115A ALA* 2.9 6.4 + - - +
116A ASN* 2.9 27.5 + - - -
72B LYS* 5.5 5.2 + - - -
640D PRO 5.1 4.5 - - - +
641D THR* 4.1 15.5 - - + -
643D GLU 4.8 6.5 - - - +
644D GLU* 3.7 27.8 - - + +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY* 3.4 25.6 - - - +
104A GLN* 3.0 15.7 + - + -
105A LEU* 3.8 18.6 - - + +
109A SER 3.3 11.8 + - - +
110A TYR* 3.3 10.1 + - - +
112A GLU* 1.3 77.7 - - - +
114A ILE* 1.3 62.8 + - + +
116A ASN* 3.4 1.4 + - - +
117A LEU* 3.0 34.2 + - + +
142A ALA* 5.4 0.4 - - + -
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Residues in contact with ILE 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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110A TYR 3.0 14.5 + - - +
111A ASP 3.6 4.7 + - - +
112A GLU 3.3 0.2 - - - -
113A ALA* 1.3 75.1 - - - +
115A ALA* 1.3 56.6 + - - +
117A LEU* 3.9 5.5 - - - -
118A GLN* 3.0 30.2 + - + +
139A LEU* 3.9 9.1 - - + +
142A ALA* 4.0 26.0 - - + +
143A LYS* 3.8 37.5 - - + -
146A ARG* 3.6 47.3 - - + +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP 3.3 6.0 + - - +
112A GLU 2.9 9.3 + - - +
114A ILE* 1.3 74.7 - - - +
116A ASN* 1.3 61.2 + - - +
118A GLN* 3.2 4.7 + - - +
119A ARG* 2.8 31.5 + - - +
641D THR* 3.2 41.3 - - + +
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Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 5.4 0.2 - - - +
97A HIS* 3.5 38.7 - - - +
100A LEU* 3.2 19.8 - - - +
101A GLY* 3.9 10.1 - - - -
104A GLN* 2.6 40.0 + - - +
112A GLU 2.9 13.2 + - - +
115A ALA* 1.3 78.3 - - - +
117A LEU* 1.3 55.6 + - - +
119A ARG* 3.3 4.6 + - - +
120A ALA* 2.8 29.5 + - - +
644D GLU* 3.7 12.4 + - - +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.7 50.5 - - + +
101A GLY* 4.2 11.0 - - - -
102A GLN* 4.5 6.5 - - + +
105A LEU* 5.6 4.5 - - + -
113A ALA* 3.0 25.1 + - + +
116A ASN* 1.3 75.8 - - - +
118A GLN* 1.3 58.4 + - - +
120A ALA* 3.5 5.5 - - - +
121A TYR* 2.9 25.6 + - - +
135A ILE* 3.7 8.4 - - + +
138A ALA* 3.7 31.9 - - + +
139A LEU* 3.6 19.9 - - + +
142A ALA* 4.1 15.9 - - + -
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Residues in contact with GLN 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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114A ILE* 3.0 22.3 + - + +
115A ALA* 3.8 4.7 - - - +
117A LEU* 1.3 75.8 - - - +
119A ARG* 1.3 62.2 + - - +
121A TYR* 3.1 30.4 + - - +
122A SER* 2.9 35.3 + - - +
139A LEU* 3.2 26.0 - - + +
143A LYS* 5.4 5.2 + - - -
537D PHE* 6.0 0.8 - - - -
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY 4.3 8.5 + - - -
92A GLN* 3.9 15.0 - - - +
97A HIS* 3.8 31.8 + - + +
115A ALA 2.8 18.1 + - - +
116A ASN* 3.7 6.3 - - - +
117A LEU 3.3 0.2 - - - -
118A GLN* 1.3 76.0 - - - +
120A ALA* 1.3 63.9 + - - +
122A SER* 3.4 12.3 + - - +
123A LEU* 3.2 58.1 + - - +
126A GLU* 4.3 13.1 + - - -
130B ASN* 3.6 54.2 + - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 3.8 33.5 - - + +
97A HIS* 4.0 6.7 - - + +
98A PHE* 4.0 20.0 - - + +
116A ASN 2.8 17.8 + - - +
117A LEU* 3.5 9.6 - - - +
119A ARG* 1.3 77.4 - - - +
121A TYR* 1.3 60.4 + - - +
123A LEU* 3.4 3.5 + - - -
124A ALA* 3.1 25.6 + - - +
135A ILE* 4.3 2.7 - - + -
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU 2.9 17.9 + - - +
118A GLN* 3.1 30.5 + - - +
120A ALA* 1.3 78.7 - - - +
122A SER* 1.3 62.7 + - - +
124A ALA* 3.7 2.6 + - + +
125A LYS* 3.5 34.5 + - + +
135A ILE* 3.5 31.8 - - + +
136A PRO* 4.2 12.3 - - + -
139A LEU* 4.5 6.1 - - + -
537D PHE* 2.8 61.3 - + - +
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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
----------------------------------------------------------
118A GLN* 2.9 23.5 + - - +
119A ARG* 3.4 19.9 + - - -
121A TYR* 1.3 77.6 - - - +
123A LEU* 1.3 65.3 + - - +
125A LYS* 3.3 10.7 + - - +
126A GLU* 3.2 31.7 + - - +
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Residues in contact with LEU 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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92A GLN* 3.5 40.8 - - - +
93A SER 3.8 7.0 - - - +
94A VAL* 3.5 16.2 - - + +
97A HIS* 3.6 30.5 - - + +
119A ARG* 3.2 52.0 + - - +
121A TYR 3.4 0.4 - - - -
122A SER* 1.3 78.1 - - - +
124A ALA* 1.3 64.2 + - - +
126A GLU* 2.9 16.5 + - - +
127A GLN* 2.9 34.4 + - - +
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Residues in contact with ALA 124 (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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94A VAL* 3.4 15.8 - - + +
120A ALA 3.1 14.4 + - - +
121A TYR* 4.2 3.4 - - + +
123A LEU* 1.3 79.0 - - - +
125A LYS* 1.3 61.1 + - - +
127A GLN* 4.6 0.4 - - - +
128A ARG 3.1 2.6 + - - -
129A LEU* 2.8 51.0 + - + +
131A PHE* 4.7 5.2 - - + -
135A ILE* 4.0 19.1 - - + -
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Residues in contact with LYS 125 (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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121A TYR* 3.5 28.6 + - + +
122A SER* 3.3 12.0 + - - +
123A LEU 3.1 0.6 - - - -
124A ALA* 1.3 79.8 - - - +
126A GLU* 1.3 64.0 + - + +
128A ARG* 3.1 17.1 + - - +
129A LEU 5.5 0.9 - - - -
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Residues in contact with GLU 126 (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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92A GLN* 5.1 7.6 + - - +
119A ARG* 4.3 12.8 + - - -
122A SER* 3.2 20.3 + - - +
123A LEU* 2.9 20.4 + - - +
125A LYS* 1.3 79.8 - - + +
127A GLN* 1.3 64.2 + - + +
128A ARG* 3.1 13.5 + - - +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 2.9 36.3 + - - +
94A VAL* 4.3 4.8 - - - +
123A LEU* 2.9 33.6 + - - +
126A GLU* 1.3 78.2 + - + +
128A ARG* 1.3 69.6 + - - +
129A LEU* 3.2 35.6 + - + +
614C ALA 4.8 5.4 + - - +
615C GLY* 3.4 25.2 + - - +
618C PRO* 4.8 1.6 - - - +
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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
------------------------------------------------------------
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