Contacts of the helix formed by residues 134 - 150 (chain B) in PDB entry 3K3B
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 GLY 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLN* 3.7 5.6 - - - -
114B THR 3.5 7.4 - - - -
116B GLU 2.9 29.2 + - - -
117B GLY* 3.2 6.5 - - - -
133B ALA* 1.3 73.4 - - - +
135B ILE* 1.3 65.5 + - - -
136B ILE 3.4 2.7 - - - -
137B PRO* 3.2 7.2 - - - +
138B ARG* 3.0 26.0 - - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN 6.1 0.4 - - - +
81B VAL* 4.2 9.4 - - + -
82B TYR* 4.9 5.2 - - + +
86B VAL* 3.7 28.9 - - + -
101B ILE* 4.4 4.9 - - + -
114B THR* 2.9 30.6 + - + +
115B MET* 3.4 18.0 + - - +
134B GLY* 1.3 71.6 - - - -
136B ILE* 1.3 57.2 + - - +
138B ARG* 3.8 5.2 - - - +
139B THR* 2.7 44.1 + - - +
263B LEU* 3.7 29.4 - - + -
333B ILE* 3.6 31.0 - - + -
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B MET* 2.9 29.0 + - + +
116B GLU* 4.4 3.8 - - + +
135B ILE* 1.3 76.2 - - - +
137B PRO* 1.4 66.7 - - + +
139B THR* 3.7 1.4 - - - -
140B LEU* 3.1 27.7 + - + +
214B LEU* 3.8 19.7 - - + -
239B PHE* 3.7 37.0 - - + -
263B LEU* 3.5 37.2 - - + +
265B ASP* 6.4 1.1 - - + -
372B L31 3.6 33.0 - - + -
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Residues in contact with PRO 137 (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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116B GLU 3.2 24.9 - - - +
127B TRP* 3.5 17.5 - - + +
133B ALA* 4.3 4.3 - - + -
134B GLY 3.2 15.0 - - - +
136B ILE* 1.4 97.6 - - + +
138B ARG* 1.3 55.4 + - - +
140B LEU* 3.4 3.4 + - + +
141B HIS* 3.0 30.3 + - - +
214B LEU* 4.3 9.2 - - + -
372B L31 3.5 46.9 - - + +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN* 3.5 12.9 - - - +
79B ILE* 3.6 36.0 - - - +
82B TYR* 3.6 38.8 - - + +
128B GLU 5.9 1.2 + - - -
130B ASP 3.7 8.5 + - - -
131B PRO* 3.1 36.8 + - - +
133B ALA* 2.8 24.4 + - + -
134B GLY 3.0 23.3 + - - +
135B ILE* 3.8 0.4 - - - +
136B ILE 3.3 0.4 - - - -
137B PRO* 1.3 80.1 - - - +
139B THR* 1.3 57.7 + - - +
141B HIS* 3.4 7.5 + - - +
142B GLN* 3.0 33.2 + - + +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.5 9.2 - - - -
86B VAL* 3.4 23.7 - - + +
90B LEU* 3.9 19.0 - - + +
135B ILE* 2.7 29.1 + - - +
136B ILE 3.7 3.6 - - - -
138B ARG* 1.3 76.3 - - - +
140B LEU* 1.3 58.6 + - + +
142B GLN* 3.1 2.8 + - - +
143B ILE* 2.9 41.8 + - + +
241B VAL* 4.9 3.4 - - + -
261B LEU* 3.6 28.1 - - + +
263B LEU* 4.6 5.8 - - + -
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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
----------------------------------------------------------
127B TRP* 5.2 1.1 - - - -
136B ILE* 3.1 26.9 + - + +
137B PRO* 3.9 3.8 - - + +
139B THR* 1.3 78.0 - - - +
141B HIS* 1.3 55.5 + - - +
143B ILE* 3.6 7.6 + - + +
144B PHE* 2.8 38.5 + - + -
156B VAL* 4.5 7.2 - - + -
158B VAL* 3.9 15.3 - - + -
204B VAL* 5.5 2.9 - - + -
210B VAL* 4.4 28.5 - - + -
214B LEU* 4.2 10.3 - - + -
239B PHE* 3.7 26.5 - - + -
241B VAL* 3.8 34.3 - - + -
263B LEU* 6.2 0.9 - - + -
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 4.1 15.2 - - + -
128B GLU* 3.6 52.9 + - + +
129B GLU* 4.4 8.1 + - - -
137B PRO 3.0 18.3 + - - +
138B ARG* 3.5 7.4 - - - +
140B LEU* 1.3 77.6 - - - +
142B GLN* 1.3 68.4 + - + +
144B PHE* 3.3 8.9 + - - +
145B GLU* 3.0 63.4 + - + +
207B LYS* 4.8 6.1 - - + +
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Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.0 39.9 - - + +
87B CYS* 6.1 1.4 - - - -
90B LEU* 3.7 7.2 - - + -
138B ARG* 3.0 15.6 + - + +
139B THR 3.1 2.7 + - - +
141B HIS* 1.3 92.3 - - + +
143B ILE* 1.3 58.3 + - - +
145B GLU* 3.9 12.1 - - - +
146B LYS* 2.7 61.7 + - + +
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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
----------------------------------------------------------
90B LEU* 3.7 21.3 - - + +
94B ILE* 5.1 2.5 - - + -
139B THR* 2.9 36.0 + - + +
140B LEU* 3.8 11.9 - - + +
141B HIS 3.4 0.2 - - - -
142B GLN* 1.3 75.1 - - - +
144B PHE* 1.3 61.2 + - + +
146B LYS* 5.0 1.3 - - - -
147B LEU* 3.2 46.1 + - + +
154B PHE* 4.2 1.6 - - + -
156B VAL* 3.8 27.6 - - + -
241B VAL* 3.7 24.9 - - + -
243B ILE* 3.5 26.0 - - + -
261B LEU* 6.2 0.2 - - + -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 2.8 30.3 - - + -
141B HIS 3.3 6.6 + - - +
142B GLN 3.1 0.4 - - - -
143B ILE* 1.3 78.6 - - + +
145B GLU* 1.3 56.8 + - - +
148B THR* 2.6 43.8 + - - +
154B PHE* 3.7 27.6 - + - -
156B VAL* 3.8 20.4 - - + -
204B VAL* 3.5 43.3 - - + -
205B HIS 4.1 4.3 - - - -
206B ASN* 3.7 19.5 - - - -
207B LYS* 4.1 25.6 - - + -
210B VAL* 4.1 9.6 - - + -
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B HIS* 3.0 57.8 + - + +
142B GLN* 3.2 17.5 + - - +
144B PHE* 1.3 81.0 - - - +
146B LYS* 1.3 57.7 + - - +
148B THR* 3.8 3.7 - - - +
149B ASP* 2.9 31.6 + - - +
207B LYS* 5.2 4.9 - - - +
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Residues in contact with LYS 146 (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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82B TYR* 5.3 0.2 - - - +
87B CYS* 5.6 2.2 - - - +
90B LEU* 3.9 21.5 - - + -
91B ASP* 3.6 25.5 + - - +
94B ILE* 3.2 34.6 - - + +
142B GLN* 2.7 44.8 + - - +
143B ILE 4.5 0.2 - - - +
145B GLU* 1.3 72.9 - - - +
147B LEU* 1.3 59.4 + - + +
149B ASP* 3.1 7.5 + - - +
150B ASN* 3.0 36.4 + - - +
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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
----------------------------------------------------------
94B ILE* 3.6 41.5 - - + -
143B ILE* 3.2 25.7 + - + +
146B LYS* 1.3 76.8 - - + +
148B THR* 1.3 61.5 + - - +
150B ASN* 3.3 16.5 - - - +
152B THR* 3.0 42.9 + - - +
154B PHE* 3.8 28.3 - - + -
243B ILE* 3.5 32.3 - - + -
245B MET* 3.9 11.4 - - - -
257B LYS* 5.6 0.9 - - - +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 2.6 28.6 + - - +
145B GLU* 3.8 3.8 - - - +
147B LEU* 1.3 76.1 - - - +
149B ASP* 1.3 68.4 + - - +
151B GLY* 3.3 11.1 + - - -
154B PHE* 3.8 16.1 - - - -
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Residues in contact with ASP 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 GLU 2.9 20.2 + - - +
146B LYS* 3.1 7.4 + - - +
148B THR* 1.3 80.8 - - - +
150B ASN* 1.3 63.7 + - - +
151B GLY* 3.2 4.5 + - - -
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Residues in contact with ASN 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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94B ILE* 5.3 4.6 - - - +
146B LYS* 3.0 20.8 + - - +
147B LEU* 3.3 24.7 - - - +
149B ASP* 1.3 79.6 - - - +
151B GLY* 1.3 62.7 + - - +
152B THR* 2.9 23.0 + - - -
247B GLU* 5.2 10.3 + - - +
257B LYS* 6.2 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
------------------------------------------------------------
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