Contacts of the helix formed by residues 134 - 152 (chain B) in PDB entry 3KYB
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLN* 1.3 82.9 - - + +
135B PHE* 1.3 59.7 + - - +
136B GLU* 3.5 5.9 + - - +
137B GLU* 2.9 36.1 + - - +
138B GLN 2.8 26.0 + - - -
165B SER* 3.1 37.6 - - - +
167B LEU 3.2 6.7 - - - +
169B ALA* 3.4 12.3 - - - +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 1.3 69.3 - - - +
136B GLU* 1.3 62.3 + - - +
138B GLN* 3.1 1.9 + - - -
139B ALA* 2.8 27.1 + - + +
148B TYR* 6.0 0.7 - + - -
152B PHE* 4.0 16.2 - + + -
156B THR* 3.3 31.9 - - + -
160B TRP* 5.2 3.4 - - - -
164B PRO* 3.2 25.4 - - + +
167B LEU* 2.7 35.1 + - + +
168B PRO 3.5 14.3 - - - +
169B ALA* 4.1 3.1 - - - +
171B ILE* 3.5 19.1 - - + -
172B LEU* 3.7 31.4 - - + -
394B FMN 3.8 28.9 - + - -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.3 5.6 - - - +
135B PHE* 1.3 74.8 - - - +
137B GLU* 1.3 62.6 + - + +
139B ALA* 3.2 2.1 + - - +
140B LEU* 2.8 45.2 + - + +
148B TYR* 2.7 42.2 + - + +
153B LYS* 4.1 13.9 + - - -
164B PRO* 3.0 14.7 + - - +
165B SER* 3.6 31.6 + - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 4.0 22.6 - - + +
131B ASP 5.5 0.4 - - - -
132B PRO* 3.8 17.9 - - + +
133B GLN* 2.9 35.9 + - - +
134B THR* 2.9 31.9 + - - +
136B GLU* 1.3 78.4 - - + +
138B GLN* 1.3 58.0 + - - +
140B LEU* 3.9 7.9 - - + +
141B ARG* 2.9 30.5 + - - +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PRO* 3.8 8.9 - - - +
134B THR 2.8 17.8 + - - +
135B PHE 3.6 3.6 - - - +
137B GLU* 1.3 78.9 - - - +
139B ALA* 1.3 57.6 + - - +
141B ARG* 3.4 36.0 + - - +
142B PHE* 3.0 49.9 + - + +
169B ALA* 3.7 26.6 - - + +
172B LEU* 3.0 34.1 - - + +
173B LYS* 5.7 0.7 - - - -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 2.8 32.2 + - + +
136B GLU 3.7 0.2 - - - +
138B GLN* 1.3 70.4 - - - +
140B LEU* 1.4 60.4 + - - +
142B PHE* 3.1 6.6 + - - +
143B ILE* 2.9 42.4 + - + +
148B TYR* 3.4 32.5 - - + -
152B PHE* 4.9 8.3 - - + -
172B LEU* 4.6 6.4 - - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASP* 3.0 21.1 + - + +
129B ILE* 3.8 20.9 - - + -
136B GLU* 2.8 41.3 + - + +
137B GLU* 4.8 2.2 - - + -
139B ALA* 1.4 75.8 - - - +
141B ARG* 1.3 64.2 + - - +
144B GLY* 3.0 21.9 + - - +
145B LYS* 3.6 39.0 - - + +
148B TYR* 3.7 20.9 - - + -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLY* 3.1 17.5 - - - -
126B ASP 3.3 22.0 + - - +
127B SER* 5.1 4.9 - - - +
129B ILE* 3.5 23.5 + - + +
130B ALA* 5.6 0.4 - - - +
131B ASP 4.8 4.0 - - - +
132B PRO* 3.6 27.0 - - + +
137B GLU 2.9 18.5 + - - +
138B GLN* 3.4 26.3 + - - +
140B LEU* 1.3 76.7 - - - +
142B PHE* 1.3 75.0 + - + +
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Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.6 10.0 - - - +
122B ALA* 5.5 1.0 - - - -
125B GLY* 3.9 5.1 - - - -
138B GLN* 3.0 45.8 + - + +
139B ALA* 3.1 4.9 + - - +
141B ARG* 1.3 91.7 - - + +
143B ILE* 1.3 59.4 + - - +
172B LEU* 3.6 22.2 - - + -
173B LYS 3.9 12.1 - - - -
174B ARG* 3.5 19.3 - - - -
175B LEU* 3.3 58.7 - - + +
176B PRO* 4.2 10.3 - - + -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 5.0 2.2 - - + -
108B PHE* 5.6 0.3 - - - -
121B ILE* 4.1 9.1 - - + +
124B LYS* 3.7 14.0 - - - +
125B GLY* 4.2 5.4 - - - -
139B ALA* 2.9 24.7 + - + +
142B PHE* 1.3 79.9 - - + +
144B GLY* 1.3 66.6 + - - +
147B LEU* 3.6 41.1 + - + +
148B TYR* 3.8 9.4 - - + +
152B PHE* 3.4 37.0 - - + -
175B LEU* 3.8 18.6 - - + -
176B PRO* 3.8 13.2 - - + -
177B VAL* 4.0 15.3 - - + -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 3.1 25.2 + - - -
125B GLY* 3.9 0.4 - - - -
126B ASP* 4.4 2.2 - - - -
140B LEU* 3.0 22.2 + - - -
143B ILE* 1.3 81.5 - - - +
145B LYS* 1.3 63.8 + - - -
146B GLU 3.5 2.0 - - - -
148B TYR* 3.1 24.9 + - - +
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASP* 6.0 0.2 - - - +
140B LEU* 3.6 20.7 - - + +
144B GLY* 1.3 69.8 - - - -
146B GLU* 1.3 66.4 + - + +
149B GLU* 2.8 74.4 + - + +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.7 21.1 - - + -
108B PHE* 3.6 13.4 - - + -
124B LYS* 2.8 36.3 + - - +
144B GLY 3.5 0.4 - - - -
145B LYS* 1.3 82.5 - - + +
147B LEU* 1.3 57.4 + - - +
149B GLU* 4.1 2.3 - - - +
150B ALA* 3.0 31.2 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.9 7.2 - - + -
103B THR* 5.8 0.4 - - + -
104B ILE* 4.6 13.2 - - + -
107B PHE* 3.8 20.6 - - + -
108B PHE* 3.9 18.2 - - + -
121B ILE* 3.6 31.0 - - + -
143B ILE* 3.6 40.7 + - + +
144B GLY 3.8 1.8 + - - -
145B LYS 3.4 0.2 - - - -
146B GLU* 1.3 74.7 - - - +
148B TYR* 1.3 67.0 + - - +
151B PHE* 2.9 60.9 + - + +
152B PHE* 3.8 1.0 - - - -
177B VAL* 5.2 1.8 - - + -
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 6.0 0.7 - + - -
136B GLU* 2.7 41.9 + - + +
139B ALA* 3.4 31.4 - - + -
140B LEU* 3.7 22.9 - - + -
143B ILE* 3.8 4.6 - - + +
144B GLY 3.1 20.0 + - - +
145B LYS 3.8 0.9 - - - +
147B LEU* 1.3 78.7 - - - +
149B GLU* 1.3 69.2 + - + +
152B PHE* 3.0 29.4 + - + +
153B LYS* 2.9 50.4 + - + +
164B PRO* 2.9 37.9 - - + +
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS* 2.8 61.5 + - + +
146B GLU* 4.1 3.0 - - - +
148B TYR* 1.3 90.9 - - + +
150B ALA* 1.3 64.0 + - - +
153B LYS* 4.1 26.5 + - + +
154B GLY* 4.4 12.6 + - - -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B VAL* 3.9 14.0 - - + +
91B ASN* 3.9 17.3 - - - +
107B PHE* 3.5 29.8 - - + -
146B GLU 3.0 18.1 + - - +
147B LEU 4.1 2.2 - - - +
149B GLU* 1.3 79.9 - - - +
151B PHE* 1.3 66.5 + - + +
154B GLY 5.5 0.5 + - - -
272B CYS* 3.3 24.3 - - - +
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Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ALA* 5.1 0.9 - - + -
90B VAL* 4.0 8.3 - - + -
95B PHE* 3.7 37.9 - + + -
97B LEU* 4.2 15.0 - - + -
99B ILE* 3.9 15.9 - - + -
103B THR* 3.5 25.4 - - + -
107B PHE* 3.6 29.4 - + - -
147B LEU* 2.9 36.9 + - + +
150B ALA* 1.3 80.6 - - + +
152B PHE* 1.4 69.8 + - + +
155B TYR* 3.9 13.5 - - - +
272B CYS* 3.9 22.4 - - - +
392B FMN 5.0 0.9 - - - +
394B FMN 2.8 23.7 + - - +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 3.5 21.8 - - + -
135B PHE* 4.0 17.3 - + + -
139B ALA* 4.9 4.0 - - + -
143B ILE* 3.4 24.0 - - + -
147B LEU 3.8 8.1 - - - -
148B TYR* 3.0 25.0 + + + +
151B PHE* 1.4 85.8 - - + +
153B LYS* 1.3 61.5 + - - +
154B GLY 3.5 1.6 - - - -
155B TYR 4.0 1.1 - - - -
156B THR* 2.7 39.8 + - - +
172B LEU* 4.4 11.2 - - + -
176B PRO* 3.6 32.3 - - + -
394B FMN 3.3 50.9 - + - +
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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