Contacts of the helix formed by residues 138 - 154 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 5.2 0.7 - - - -
136A PRO* 3.4 10.4 - - - +
137A LYS* 1.3 81.7 - - - +
139A GLU* 1.3 60.1 + - - +
140A GLN* 2.9 39.5 + - + +
141A GLY* 2.7 26.1 + - - +
169A ASN* 3.3 37.2 + - + -
558A THR* 4.9 4.0 - - + -
559A GLU* 3.3 10.1 + - - +
138B HIS* 5.7 1.3 + + - -
140B GLN* 2.9 26.9 + - - -
555B MET* 3.3 47.5 - - + +
556B THR* 4.8 0.7 - - + -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 3.5 23.8 - - + +
136A PRO* 4.6 1.8 - - - -
138A HIS* 1.3 71.4 + - - +
140A GLN* 1.3 60.8 + - - +
142A ALA* 2.9 20.6 + - - +
143A GLY 3.0 9.9 + - - -
161A VAL* 3.7 22.4 - - + -
162A THR* 4.9 1.2 - - - +
166A GLY* 3.7 15.2 - - - +
169A ASN* 3.2 32.6 - - + +
170A VAL* 3.8 17.4 - - + +
555B MET* 3.6 5.5 - - - +
1700B TPP 2.5 41.9 + - - +
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A HIS* 2.9 24.4 + - + +
139A GLU* 1.3 76.2 - - - +
141A GLY* 1.3 63.4 + - - +
143A GLY 3.1 1.7 + - - -
144A HIS* 3.0 53.8 + - + +
169A ASN 3.4 15.5 + - - +
172A THR* 4.1 4.6 - - - +
173A PRO* 3.6 17.1 - - + +
524A THR* 4.3 6.9 - - - +
525A MET 4.8 3.0 + - - -
556A THR* 4.4 16.7 - - + +
138B HIS* 2.9 33.9 + - - -
169B ASN* 4.1 16.6 + - - +
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Residues in contact with GLY 141 (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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136A PRO* 4.0 2.2 - - - -
138A HIS* 2.7 13.1 + - - +
140A GLN* 1.3 80.0 - - - +
142A ALA* 1.3 54.5 + - - -
144A HIS* 3.3 1.5 + - - -
145A MET* 2.8 39.4 + - - +
530A PRO* 3.9 13.3 - - - +
556A THR* 6.1 2.6 - - - +
559A GLU* 3.6 22.7 + - - -
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Residues in contact with ALA 142 (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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111A PHE* 3.7 9.9 - - + +
112A GLY* 4.0 25.6 - - - +
136A PRO* 3.6 17.7 - - + +
138A HIS 3.4 4.0 + - - -
139A GLU* 2.9 14.0 + - + +
141A GLY* 1.3 75.8 - - - +
143A GLY* 1.3 58.2 + - - +
145A MET* 3.3 14.3 + - - +
146A ALA* 2.9 29.8 + - - +
159A VAL* 4.4 9.0 - - + -
161A VAL* 5.1 0.7 - - + -
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Residues in contact with GLY 143 (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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139A GLU 3.0 11.6 + - - -
140A GLN 3.1 3.1 + - - -
142A ALA* 1.3 76.1 - - - +
144A HIS* 1.3 61.5 + - - +
146A ALA 3.2 1.2 + - - -
147A GLU* 3.1 8.0 + - - +
159A VAL* 4.1 16.5 - - - +
170A VAL* 5.3 3.8 - - - -
173A PRO* 3.6 21.8 - - - -
184A MET* 3.0 24.8 - - - +
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Residues in contact with HIS 144 (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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140A GLN* 3.0 54.9 + - + +
141A GLY* 5.2 0.2 - - - -
143A GLY* 1.3 73.3 - - - +
145A MET* 1.3 65.6 + - - +
147A GLU* 2.8 32.4 + - - +
148A GLY 3.0 18.4 + - - -
172A THR* 4.1 3.5 - - + +
173A PRO* 3.8 18.4 - - + +
176A ASP* 4.3 4.3 - - + -
524A THR* 3.8 22.1 - - + +
526A GLY 4.7 2.7 - - - -
527A TYR* 3.7 25.2 - + + -
530A PRO* 3.7 30.3 - - + -
531A ALA* 3.5 9.3 - - - +
556A THR* 5.2 1.3 - - + -
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Residues in contact with MET 145 (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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111A PHE* 3.4 33.7 - - + -
134A VAL* 3.8 19.1 - - + +
136A PRO* 3.7 24.0 - - + -
141A GLY 2.8 19.7 + - - +
142A ALA* 3.5 21.8 - - - +
144A HIS* 1.3 75.6 - - - +
146A ALA* 1.3 58.3 + - - +
148A GLY 3.2 1.6 + - - -
149A TYR* 2.9 26.3 + - - +
530A PRO* 3.2 31.0 - - + +
533A ILE* 3.9 26.5 - - + -
534A GLY* 3.3 11.3 - - - -
559A GLU* 5.2 2.9 - - - +
562A SER* 5.3 3.1 - - - -
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Residues in contact with ALA 146 (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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111A PHE* 3.9 22.4 - - + -
142A ALA 2.9 13.4 + - - +
143A GLY 3.4 9.4 - - - +
144A HIS 3.2 0.2 - - - -
145A MET* 1.3 77.2 - - - +
147A GLU* 1.3 56.6 + - - +
149A TYR* 3.3 2.3 + - - +
150A ALA* 3.0 29.1 + - - +
157A GLY* 3.8 17.6 - - - -
159A VAL* 3.5 23.3 - - + -
183A PRO 5.9 0.2 - - - -
184A MET* 3.9 6.7 - - + -
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Residues in contact with GLU 147 (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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143A GLY 3.1 3.9 + - - +
144A HIS* 2.8 39.4 + - - +
146A ALA* 1.3 75.4 - - - +
148A GLY* 1.3 65.7 + - - +
150A ALA* 3.2 1.6 + - - +
151A ARG* 3.0 29.6 + - - +
173A PRO* 3.6 16.1 - - - +
176A ASP* 2.6 27.5 - - - +
177A ALA* 3.1 20.6 + - + -
182A ILE* 3.6 18.9 - - + +
183A PRO 6.0 0.2 - - - -
184A MET* 3.2 21.3 - - + -
527A TYR* 3.7 14.0 - - + +
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Residues in contact with GLY 148 (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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144A HIS 3.0 12.4 + - - -
145A MET 3.7 1.1 - - - -
147A GLU* 1.3 77.0 - - - +
149A TYR* 1.3 62.9 + - - +
151A ARG 3.5 0.2 + - - -
152A ALA* 3.1 27.2 + - - +
517A ILE* 3.8 14.1 - - - +
527A TYR* 4.6 0.2 + - - -
531A ALA* 3.4 29.1 - - - +
535A ALA* 3.8 7.9 - - - -
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Residues in contact with TYR 149 (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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108A ASP* 3.3 16.5 + - - -
109A THR* 3.6 27.0 + - + -
111A PHE* 3.7 25.8 - + + -
145A MET 2.9 15.6 + - - +
146A ALA 3.5 4.7 - - - +
147A GLU 3.2 0.2 - - - -
148A GLY* 1.3 77.6 - - - +
150A ALA* 1.3 55.5 + - - +
152A ALA 3.5 0.2 + - - -
153A SER* 2.7 54.5 + - - -
155A LYS* 3.3 28.3 - - + +
156A PRO 4.0 21.3 - - - -
157A GLY* 4.3 4.3 - - - -
158A VAL 5.8 0.4 - - - -
534A GLY 3.5 17.6 - - - +
537A VAL* 4.5 2.7 - - + -
538A ALA* 3.5 32.3 - - + +
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Residues in contact with ALA 150 (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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146A ALA 3.0 17.2 + - - +
147A GLU 3.7 3.6 - - - +
149A TYR* 1.3 78.0 - - - +
151A ARG* 1.3 58.1 + - - +
153A SER* 3.8 0.2 - - - -
154A GLY* 2.7 31.9 + - - -
155A LYS 3.1 24.0 - - - +
157A GLY 3.9 2.5 - - - +
182A ILE* 3.8 12.1 - - + -
183A PRO* 3.7 26.8 - - + +
514A HIS* 5.2 0.2 + - - -
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Residues in contact with ARG 151 (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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147A GLU 3.0 12.7 + - - +
148A GLY 4.1 1.1 - - - +
150A ALA* 1.3 77.0 - - - +
152A ALA* 1.3 57.8 + - - +
180A ASP* 4.1 10.8 + - - -
182A ILE* 3.3 35.6 - - + +
183A PRO* 6.1 0.4 - - + -
336A GLN* 2.5 34.4 + - - +
514A HIS* 2.8 33.1 + - - +
516A PHE 3.5 17.8 + - - -
517A ILE* 4.0 20.0 - - + +
518A THR 2.6 33.1 + - - +
527A TYR* 3.3 23.0 + - - -
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Residues in contact with ALA 152 (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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148A GLY 3.1 18.2 + - - +
149A TYR 4.1 2.0 - - - +
151A ARG* 1.3 77.6 - - - +
153A SER* 1.3 59.9 + - - +
492A ILE* 4.1 15.2 - - + +
514A HIS* 4.2 17.6 - - - +
517A ILE* 3.7 16.6 - - + -
535A ALA* 3.9 17.3 - - + +
538A ALA* 4.3 6.5 - - + -
539A LYS* 3.4 21.4 - - + +
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Residues in contact with SER 153 (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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149A TYR* 2.7 30.6 + - - -
152A ALA* 1.3 81.1 - - - +
154A GLY* 1.3 61.1 + - - +
155A LYS* 3.1 38.1 + - - +
514A HIS* 5.3 2.0 - - - -
538A ALA* 3.9 16.6 - - - -
539A LYS* 4.7 7.5 + - - +
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Residues in contact with GLY 154 (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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150A ALA 2.7 17.7 + - - -
151A ARG 4.5 1.0 - - - -
152A ALA 3.9 0.6 - - - -
153A SER* 1.3 72.7 - - - +
155A LYS* 1.3 62.0 + - - +
156A PRO* 4.6 1.2 - - - +
183A PRO* 5.2 5.5 - - - +
238A THR* 6.1 0.3 - - - +
311A LEU 5.8 0.2 - - - -
514A HIS* 4.7 15.0 + - - -
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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