Contacts of the helix formed by residues 135 - 151 (chain B) in PDB entry 4KMH
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 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.8 9.0 - - + -
54B VAL* 4.1 14.0 - - + +
73B MET* 3.8 21.8 - - + -
133B PRO 4.1 7.2 - - - +
134B PRO* 1.3 75.3 - - + +
136B TRP* 1.3 64.3 + - - +
137B PRO* 3.4 2.7 - - - -
138B ALA* 3.4 17.0 - - - +
139B GLU* 3.7 5.7 + - - +
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Residues in contact with TRP 136 (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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122B PHE* 4.1 10.3 - + - -
124B LEU* 3.4 33.1 - - + +
134B PRO* 3.6 27.1 - - + +
135B THR* 1.3 76.9 + - - +
137B PRO* 1.4 94.3 - - + +
139B GLU* 3.0 11.6 + - - +
140B LEU* 3.0 25.6 + - + +
167B LEU* 3.8 23.5 - - + +
168B ASP* 3.3 46.9 + - + +
238B MET* 3.8 22.4 - - + -
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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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90B TYR* 3.5 30.3 - - + +
122B PHE* 3.6 28.3 - - + -
124B LEU* 4.2 1.1 - - + -
134B PRO 3.3 15.7 - - - +
135B THR 3.4 1.3 - - - -
136B TRP* 1.4 124.8 - - + +
138B ALA* 1.3 56.6 + - - +
140B LEU* 3.2 8.5 + - + +
141B MET* 2.9 34.9 + - - +
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Residues in contact with ALA 138 (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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54B VAL* 3.8 20.2 - - + -
71B VAL* 4.0 25.5 - - + +
73B MET* 3.6 24.2 - - + -
90B TYR* 4.6 2.0 - - - -
135B THR 3.4 12.5 + - - +
136B TRP 3.1 0.6 - - - -
137B PRO* 1.3 79.0 - - - +
139B GLU* 1.3 57.3 + - - +
141B MET* 3.3 4.7 + - - +
142B GLN* 3.0 32.9 + - - +
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Residues in contact with GLU 139 (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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66B ASP* 4.4 5.4 - - - +
135B THR 3.7 5.9 + - - +
136B TRP* 3.0 13.2 + - - +
138B ALA* 1.3 76.2 - - - +
140B LEU* 1.3 60.1 + - - +
142B GLN* 3.5 10.7 + - - +
143B GLY* 3.0 23.4 + - - -
146B ARG* 3.5 30.2 + - - -
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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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122B PHE* 5.1 7.4 - - + -
136B TRP* 3.0 30.7 + - + +
137B PRO* 3.4 14.1 - - + +
139B GLU* 1.3 77.1 - - - +
141B MET* 1.3 58.6 + - + +
143B GLY* 3.1 3.7 + - - -
144B LEU* 2.9 27.8 + - + +
163B TRP* 3.9 32.2 - - + +
167B LEU* 4.0 31.0 - - + +
177B MET* 3.9 28.7 - - + -
200B ILE* 4.8 14.1 - - + -
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Residues in contact with MET 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.6 13.6 - - + +
71B VAL* 4.1 12.3 - - + -
90B TYR* 3.9 30.7 - - - +
91B ILE 4.1 1.3 - - - -
92B SER* 3.5 27.4 - - - +
120B LEU* 3.2 45.9 - - + +
121B THR* 4.1 2.5 - - - +
122B PHE* 4.6 6.7 - - + -
137B PRO 2.9 20.5 + - - +
138B ALA 3.3 4.7 + - - +
140B LEU* 1.3 73.6 - - + +
142B GLN* 1.3 59.9 + - - +
144B LEU* 3.2 3.7 + - - +
145B ALA* 2.8 31.0 + - - +
200B ILE* 3.9 19.5 - - + -
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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
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54B VAL* 5.0 11.0 + - + +
55B THR* 5.9 0.4 - - - +
56B ALA* 5.1 3.8 - - - +
66B ASP* 3.2 29.1 - - - +
67B PRO* 3.4 4.7 - - - +
68B LEU* 3.1 55.4 + - - +
69B ASP 5.5 0.4 - - - -
71B VAL* 4.3 11.3 - - - +
138B ALA 3.0 22.7 + - - +
139B GLU* 3.5 24.0 - - - +
141B MET* 1.3 74.7 - - - +
143B GLY* 1.3 62.0 + - - +
145B ALA* 3.2 5.2 + - - +
146B ARG* 3.1 32.4 + - - +
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Residues in contact with GLY 143 (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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139B GLU 3.0 13.8 + - - -
140B LEU* 3.1 4.7 + - - -
142B GLN* 1.3 77.6 - - - +
144B LEU* 1.3 58.8 + - - +
146B ARG* 3.2 34.8 + - - +
147B TYR* 3.5 5.7 + - - +
163B TRP* 4.1 19.6 - - - -
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Residues in contact with LEU 144 (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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118B PHE* 6.4 0.2 - - + -
120B LEU* 3.9 17.7 - - + -
140B LEU* 2.9 14.5 + - + +
141B MET 3.7 4.5 - - - +
143B GLY* 1.3 76.0 - - - +
145B ALA* 1.3 63.4 + - - +
147B TYR* 3.3 13.9 + - + +
148B VAL* 3.3 15.0 - - + +
155B PHE* 3.7 32.5 - - + -
161B VAL* 4.7 8.7 - - + -
163B TRP* 4.2 10.6 - - + -
177B MET* 3.7 37.9 - - + -
179B LEU* 4.9 5.2 - - + -
200B ILE* 3.8 27.1 - - + -
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Residues in contact with ALA 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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67B PRO* 3.9 14.4 - - + -
68B LEU* 3.9 27.1 - - + -
95B LEU* 4.5 10.3 - - + -
120B LEU* 4.7 0.2 - - - +
141B MET 2.8 17.9 + - - +
142B GLN 3.2 6.3 + - - +
144B LEU* 1.3 75.4 - - - +
146B ARG* 1.3 59.6 + - - +
148B VAL* 3.3 8.2 + - - +
149B PHE* 3.0 40.1 + - + -
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Residues in contact with ARG 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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60B TYR* 6.0 0.9 - - + -
65B PRO* 3.0 33.8 + - - +
66B ASP* 2.7 29.4 + - - -
67B PRO* 4.1 9.0 - - + -
139B GLU* 3.5 19.4 + - - -
142B GLN* 3.1 18.5 + - - +
143B GLY* 3.3 36.7 - - - +
144B LEU 3.2 0.4 - - - -
145B ALA* 1.3 74.3 - - - +
147B TYR* 1.3 58.7 + - - +
149B PHE* 4.1 2.2 - - - +
150B GLN* 3.0 56.8 + - - +
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Residues in contact with TYR 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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143B GLY 3.5 5.5 + - - +
144B LEU* 3.3 18.1 + - + +
146B ARG* 1.3 78.5 - - - +
148B VAL* 1.3 61.4 + - + +
150B GLN* 4.3 3.6 - - - +
151B SER* 2.9 34.1 + - - -
153B ASN* 4.4 17.7 - - + -
155B PHE* 4.2 23.1 - + - -
161B VAL* 5.1 13.9 - - + -
162B SER 5.6 4.3 - - - -
163B TRP* 4.8 15.9 - + - -
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Residues in contact with VAL 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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95B LEU* 3.9 28.0 - - + -
116B PHE* 3.5 29.8 - - + -
118B PHE* 4.4 11.2 - - + -
120B LEU* 6.2 0.2 - - + -
144B LEU* 3.3 20.9 - - + +
145B ALA 3.3 6.3 + - - +
146B ARG 3.3 0.8 - - - -
147B TYR* 1.3 77.0 - - - +
149B PHE* 1.3 54.4 + - - +
151B SER* 2.7 29.7 + - - +
152B GLU* 3.7 1.9 - - - -
153B ASN 3.9 17.2 + - - +
155B PHE* 4.1 27.8 - - + -
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Residues in contact with PHE 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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60B TYR* 3.5 36.5 + + + +
67B PRO* 3.7 23.6 - - + -
94B GLY 3.6 21.5 - - - -
95B LEU* 3.7 28.0 - - + -
104B VAL* 3.7 27.8 - - + -
105B HIS* 3.7 17.0 - + - -
116B PHE* 4.0 14.7 - + - -
145B ALA* 3.0 30.0 + - + +
146B ARG* 4.1 4.5 - - - +
148B VAL* 1.3 73.2 - - - +
150B GLN* 1.3 60.9 + - + +
151B SER 2.9 13.1 - - - +
152B GLU* 5.1 1.7 - - - +
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Residues in contact with GLN 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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153A ASN* 4.3 9.4 + - - +
60B TYR* 5.4 4.7 - - - +
146B ARG* 3.0 41.8 + - - +
147B TYR* 4.3 4.7 - - - +
149B PHE* 1.3 74.8 - - + +
151B SER* 1.3 61.1 + - - +
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Residues in contact with SER 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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151A SER* 4.3 14.6 - - - -
153A ASN* 4.2 11.2 - - - +
147B TYR* 2.9 21.1 + - - -
148B VAL 2.7 16.3 + - - +
149B PHE 2.9 13.2 - - - +
150B GLN* 1.3 77.2 - - - +
152B GLU* 1.3 66.4 + - - +
153B ASN* 3.3 35.3 + - - +
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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