Contacts of the helix formed by residues 138 - 154 (chain B) in PDB entry 1JSC
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 HIS 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A HIS* 5.7 0.8 + + - -
140A GLN* 2.9 28.7 + - - -
555A MET* 3.4 44.8 - - + +
556A THR* 4.8 0.7 - - + -
113B TYR* 5.3 0.9 - - - -
136B PRO* 3.4 10.9 - - - +
137B LYS* 1.3 80.6 - - - +
139B GLU* 1.3 57.1 + - - +
140B GLN* 2.9 39.9 + - + +
141B GLY* 2.7 30.1 + - - +
169B ASN* 3.3 36.1 + - + -
558B THR* 4.7 4.7 - - + -
559B GLU* 3.1 9.9 + - - +
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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
----------------------------------------------------------
555A MET* 3.6 5.5 - - - +
700A TPP 2.7 38.2 + - - +
113B TYR* 3.5 25.9 - - + +
136B PRO* 4.5 2.0 - - - +
138B HIS* 1.3 71.3 + - - +
140B GLN* 1.3 63.2 + - - +
142B ALA* 2.9 19.8 + - - +
143B GLY 3.0 9.7 + - - -
161B VAL* 3.7 22.9 - - + -
162B THR* 4.9 1.0 - - - +
166B GLY* 3.8 15.1 - - - +
169B ASN* 3.2 32.7 - - + +
170B VAL* 3.8 17.7 - - + +
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A HIS* 2.9 32.7 + - - -
169A ASN* 4.2 9.2 + - - +
138B HIS* 2.9 23.0 + - + +
139B GLU* 1.3 78.0 - - - +
141B GLY* 1.3 63.6 + - - +
143B GLY* 3.1 2.6 + - - -
144B HIS* 3.0 53.8 + - + +
169B ASN 3.4 15.9 + - - +
172B THR* 4.1 11.0 - - - +
173B PRO* 3.6 16.2 - - + +
524B THR* 4.2 6.9 - - - +
525B MET 4.7 3.6 + - - -
556B THR* 4.3 16.4 - - + +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO* 4.0 0.2 - - - -
138B HIS* 2.7 12.5 + - - +
140B GLN* 1.3 79.4 - - - +
142B ALA* 1.3 55.8 + - - -
144B HIS* 3.3 0.8 + - - -
145B MET* 2.8 40.7 + - - +
530B PRO* 3.8 13.9 - - - +
556B THR* 5.9 2.4 - - - +
559B GLU* 3.6 23.6 + - - -
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Residues in contact with ALA 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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111B PHE* 3.6 9.6 - - + +
112B GLY* 4.0 24.7 - - - +
136B PRO* 3.6 18.5 - - + +
138B HIS 3.4 3.8 + - - -
139B GLU* 2.9 15.1 + - + +
141B GLY* 1.3 77.2 - - - +
143B GLY* 1.3 57.1 + - - +
145B MET* 3.5 14.0 - - - +
146B ALA* 2.9 29.8 + - - +
159B VAL* 4.4 9.9 - - + -
161B VAL* 5.1 0.9 - - + -
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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 10.9 + - - -
140B GLN 3.1 3.5 + - - -
142B ALA* 1.3 76.8 - - - +
144B HIS* 1.3 60.8 + - - +
146B ALA 3.3 1.2 + - - -
147B GLU* 3.1 7.8 + - - +
159B VAL* 4.1 16.2 - - - +
170B VAL* 5.3 3.4 - - - -
173B PRO* 3.6 22.2 - - - -
184B MET* 3.0 25.5 - - - +
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Residues in contact with HIS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.0 53.0 + - + +
143B GLY* 1.3 72.6 - - - +
145B MET* 1.3 66.3 + - - +
147B GLU* 2.8 31.5 + - - +
148B GLY 3.0 18.4 + - - -
172B THR* 4.1 3.3 - - + +
173B PRO* 3.8 18.8 - - + +
176B ASP* 4.4 4.3 - - + -
524B THR* 3.8 21.3 - - + +
526B GLY 4.6 2.5 - - - -
527B TYR* 3.6 24.5 - + + -
530B PRO* 3.6 32.1 - - + -
531B ALA* 3.5 10.1 - - - +
556B THR* 5.2 1.1 - - + -
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Residues in contact with MET 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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111B PHE* 3.4 32.5 - - + -
134B VAL* 3.8 18.2 - - + +
136B PRO* 3.7 23.6 - - + -
141B GLY* 2.8 19.9 + - - +
142B ALA* 3.5 21.8 - - - +
144B HIS* 1.3 75.6 - - - +
146B ALA* 1.3 58.7 + - - +
148B GLY 3.2 1.2 + - - -
149B TYR* 2.9 26.0 + - - +
530B PRO* 3.2 30.1 - - + +
533B ILE* 3.9 27.4 - - + -
534B GLY* 3.2 11.5 - - - -
559B GLU* 5.1 2.9 - - - +
562B SER* 5.1 3.1 - - - -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.8 21.5 - - + -
142B ALA 2.9 14.1 + - - +
143B GLY 3.4 9.4 - - - +
145B MET* 1.3 77.2 - - - +
147B GLU* 1.3 56.6 + - - +
149B TYR* 3.4 2.3 - - - +
150B ALA* 2.9 29.1 + - - +
157B GLY* 3.8 16.6 - - - -
159B VAL* 3.5 23.1 - - + -
184B MET* 3.9 7.6 - - + -
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Residues in contact with GLU 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 3.1 4.7 + - - +
144B HIS* 2.8 39.2 + - - +
146B ALA* 1.3 73.8 - - - +
148B GLY* 1.3 66.7 + - - +
150B ALA* 3.2 2.0 + - - +
151B ARG* 3.0 29.5 + - - +
173B PRO* 3.6 16.3 - - - +
176B ASP* 2.5 27.3 - - - +
177B ALA* 3.2 20.2 + - + -
182B ILE* 3.6 19.4 - - + +
184B MET* 3.2 21.5 - - + -
527B TYR* 3.7 13.9 - - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B HIS 3.0 11.6 + - - -
145B MET 3.2 1.3 + - - -
147B GLU* 1.3 76.7 - - - +
149B TYR* 1.3 62.8 + - - +
151B ARG 3.4 0.2 + - - -
152B ALA* 3.1 26.7 + - - +
517B ILE* 3.9 14.0 - - - +
531B ALA* 3.4 28.6 - - - +
535B ALA* 3.7 8.5 - - - -
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Residues in contact with TYR 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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108B ASP* 3.4 15.9 + - - -
109B THR* 3.5 26.2 + - + -
111B PHE* 3.6 26.2 - + + -
145B MET 2.9 15.8 + - - +
146B ALA 3.4 4.3 - - - +
148B GLY* 1.3 77.2 - - - +
150B ALA* 1.3 55.9 + - - +
153B SER* 2.7 54.4 + - - -
155B LYS* 3.3 28.8 - - + +
156B PRO 4.0 21.3 - - - -
157B GLY* 4.4 4.0 - - - -
158B VAL 5.6 0.7 - - - -
534B GLY 3.3 19.8 - - - +
537B VAL* 4.4 3.4 - - + -
538B ALA* 3.5 31.6 - - + +
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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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146B ALA 2.9 17.0 + - - +
147B GLU 3.2 4.0 + - - +
149B TYR* 1.3 78.1 - - - +
151B ARG* 1.3 57.7 + - - +
154B GLY* 2.7 32.7 + - - -
155B LYS 3.1 24.2 - - - +
157B GLY 3.9 2.9 - - - +
182B ILE* 3.9 11.7 - - + -
183B PRO* 3.6 27.4 - - + +
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Residues in contact with ARG 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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147B GLU 3.0 12.9 + - - +
148B GLY 4.1 2.9 - - - +
150B ALA* 1.3 75.8 - - - +
152B ALA* 1.3 57.4 + - - +
180B ASP* 4.1 10.3 + - - -
182B ILE* 3.3 34.9 - - + +
183B PRO* 6.1 0.2 - - + -
336B GLN* 3.3 32.5 + - - +
514B HIS* 2.9 35.1 + - - +
516B PHE 3.5 17.8 + - - -
517B ILE* 4.0 19.8 - - + +
518B THR 2.8 32.1 + - - +
527B TYR* 3.2 22.1 + - - -
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Residues in contact with ALA 152 (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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148B GLY 3.1 17.8 + - - +
149B TYR 4.1 1.8 - - - +
151B ARG* 1.3 77.4 - - - +
153B SER* 1.3 60.2 + - - +
492B ILE* 4.1 16.1 - - + +
514B HIS* 4.4 15.8 - - - +
517B ILE* 3.9 16.1 - - + +
535B ALA* 4.0 17.0 - - + +
538B ALA* 4.1 7.2 - - + -
539B LYS* 3.2 23.4 - - + +
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Residues in contact with SER 153 (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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149B TYR* 2.7 29.4 + - - -
150B ALA 3.7 0.2 + - - -
152B ALA* 1.3 81.3 - - - +
154B GLY* 1.3 59.9 + - - +
155B LYS* 3.1 39.0 + - - +
514B HIS* 5.6 1.6 - - - -
538B ALA* 3.8 17.7 - - - -
539B LYS* 4.6 7.0 + - - +
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Residues in contact with GLY 154 (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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150B ALA 2.7 17.4 + - - -
151B ARG 4.5 1.2 + - - -
152B ALA 3.8 0.4 - - - -
153B SER* 1.3 73.3 - - - +
155B LYS* 1.3 62.6 + - - +
156B PRO* 4.3 1.7 - - - +
183B PRO* 5.2 5.2 - - - +
238B THR* 6.1 0.3 - - - +
514B HIS* 5.0 12.5 + - - -
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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