Contacts of the helix formed by residues 137 - 150 (chain K) in PDB entry 1I43
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 SER 137 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110I ARG* 4.0 12.9 - - - -
292I GLY* 2.9 28.4 + - - -
294I ALA* 5.7 1.6 - - - -
135K MET* 3.2 2.0 - - - +
136K ALA* 1.3 80.3 - - - +
138K GLY* 1.3 65.7 + - - +
139K MET* 3.6 1.0 + - - +
140K CYS* 3.1 13.4 + - - +
141K ALA 3.1 14.9 + - - -
270K LEU* 4.5 6.5 - - - -
271K ALA* 3.4 9.6 - - - +
272K GLY* 3.1 15.7 - - - -
500K PLP 3.2 15.7 + - - -
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Residues in contact with GLY 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K SER* 1.3 70.7 - - - +
139K MET* 1.3 60.2 + - - -
141K ALA* 3.0 13.0 + - - +
142K SER* 2.9 18.3 + - - -
256K LEU* 4.5 2.8 - - - +
257K HIS 4.1 9.9 - - - -
258K SER* 4.0 7.4 - - - -
271K ALA 3.4 6.8 + - - -
272K GLY* 3.9 9.2 - - - -
500K PLP 2.6 30.3 + - - -
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Residues in contact with MET 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ARG* 3.2 39.7 - - - +
289I HIS 5.0 0.2 - - - +
290I ILE* 3.4 28.3 - - + +
291I LEU 3.9 2.0 - - - -
292I GLY* 4.4 0.9 - - - -
137K SER* 3.9 2.9 - - - +
138K GLY* 1.3 71.0 - - - +
140K CYS* 1.3 58.6 + - - +
142K SER* 3.4 6.9 + - - +
143K THR* 2.8 41.1 + - - +
163K TYR* 3.7 28.0 - - - -
165K LYS* 4.0 9.4 - - + +
166K THR* 3.8 32.3 - - + +
169K PHE* 5.4 2.0 - - + -
500K PLP 2.6 19.8 + - - +
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Residues in contact with CYS 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291I LEU 3.2 14.1 + - - -
292I GLY 3.3 21.5 - - - +
293I GLY* 5.1 0.9 - - - -
135K MET* 3.7 23.8 - - + -
136K ALA 4.1 2.0 - - - -
137K SER* 3.1 18.8 + - - +
138K GLY 3.1 0.2 - - - -
139K MET* 1.3 79.1 - - - +
141K ALA* 1.3 56.3 + - - +
143K THR* 4.3 0.9 - - - -
144K VAL* 2.9 45.8 + - - +
288K HIS* 5.3 0.2 - - - -
293K GLY* 4.0 23.8 - - - -
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Residues in contact with ALA 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K MET* 3.5 18.5 - - - -
137K SER 3.1 9.1 + - - +
138K GLY 3.0 10.4 + - - +
140K CYS* 1.3 73.9 - - - +
142K SER* 1.3 66.1 + - - +
144K VAL* 4.0 0.2 - - - -
145K MET* 2.8 27.7 + - - +
256K LEU* 4.3 6.3 - - + -
273K CYS 4.0 17.3 - - - +
274K ILE* 3.3 28.3 - - + +
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Residues in contact with SER 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K GLY 2.9 16.3 + - - -
139K MET* 3.8 9.1 + - - -
141K ALA* 1.3 76.0 - - - +
143K THR* 1.3 55.0 + - - +
145K MET* 3.1 4.3 + - - +
146K LEU* 2.8 44.4 + - - +
166K THR* 4.5 24.4 + - - -
205K PHE* 4.8 8.7 - - - -
236K ASP* 5.6 0.3 + - - -
256K LEU* 4.1 26.3 - - - +
500K PLP 5.1 4.7 - - - -
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Residues in contact with THR 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I ILE 3.8 14.4 + - - -
291I LEU* 3.4 37.3 - - + +
139K MET* 2.8 28.2 + - - +
140K CYS* 3.7 4.5 - - - +
142K SER* 1.3 73.1 - - - +
144K VAL* 1.3 65.6 + - + +
146K LEU* 3.2 2.6 + - - +
147K LEU* 3.0 41.2 + - + +
169K PHE* 4.0 23.7 - - + -
291K LEU* 5.2 2.5 - - + -
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Residues in contact with VAL 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K MET* 3.4 26.7 - - + -
140K CYS* 2.9 36.6 + - - +
143K THR* 1.3 75.6 - - + +
145K MET* 1.3 66.5 + - - +
147K LEU* 3.4 4.4 + - - -
148K ALA* 3.0 23.2 + - - +
284K ILE* 3.6 21.5 - - + +
287K LEU* 3.6 13.8 - - + +
288K HIS* 4.2 13.5 - - - +
291K LEU* 3.9 22.0 - - + -
293K GLY* 6.4 0.4 - - - +
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Residues in contact with MET 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ALA 2.8 20.3 + - - +
142K SER* 3.9 7.0 - - - +
144K VAL* 1.3 76.7 - - - +
146K LEU* 1.3 99.2 + - + +
148K ALA* 4.0 0.2 - - - -
149K LEU* 3.1 41.9 + - + +
150K VAL* 5.2 0.2 - - + -
203K LEU* 3.7 31.9 - - + -
205K PHE* 4.5 8.5 - - + -
234K CYS* 4.0 21.8 - - - -
254K LEU* 4.7 5.4 - - + -
256K LEU* 4.5 7.6 - - + -
274K ILE* 3.8 16.6 - - + -
284K ILE* 4.1 18.3 - - + +
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Residues in contact with LEU 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K SER* 2.8 26.2 + - - +
143K THR 3.5 4.0 - - - +
145K MET* 1.3 95.6 - - + +
147K LEU* 1.3 62.1 + - - +
148K ALA 3.0 1.6 + - - -
150K VAL* 3.1 34.4 + - + +
156K ILE* 3.3 32.8 - - + -
166K THR* 4.7 9.0 - - + -
169K PHE* 3.6 33.7 - - + -
170K ILE* 4.0 20.0 - - + -
174K LEU* 4.2 9.7 - - + +
203K LEU* 4.1 2.0 - - + -
205K PHE* 5.2 7.4 - - + -
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Residues in contact with LEU 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I LEU* 5.2 13.9 - - + -
173I ILE* 5.9 7.4 - - + -
176I LYS* 4.2 17.0 + - - -
291I LEU* 5.1 3.8 - - + -
143K THR* 3.0 35.2 + - + +
146K LEU* 1.3 76.3 - - - +
148K ALA* 1.3 58.4 + - - +
150K VAL 4.3 7.5 - - - +
169K PHE* 3.8 21.1 - - + -
173K ILE* 5.5 6.1 - - + -
174K LEU* 4.3 7.4 - - + -
177K MET* 3.9 34.3 - - + +
287K LEU* 3.7 18.5 - - + +
291K LEU* 4.2 17.5 - - + -
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Residues in contact with ALA 148 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176I LYS* 5.7 2.2 + - - +
144K VAL 3.0 17.9 + - - +
145K MET 4.0 2.2 - - - +
146K LEU 3.0 0.2 - - - -
147K LEU* 1.3 80.2 - - - +
149K LEU* 1.3 66.0 + - + +
150K VAL 3.7 1.4 - - - +
283K GLU* 4.2 13.8 - - - +
284K ILE* 4.0 28.9 - - + +
287K LEU* 3.7 17.0 - - + -
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Residues in contact with LEU 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K MET* 3.1 35.1 + - + +
148K ALA* 1.3 81.5 - - - +
150K VAL* 1.3 67.8 + - + +
151K PRO* 3.3 12.1 - - - +
202K ASN* 5.5 1.3 + - - +
203K LEU* 4.5 8.7 - - + -
232K LEU* 4.6 14.3 - - + +
254K LEU* 3.4 32.3 - - + -
280K LEU* 4.1 27.1 - - + +
283K GLU* 4.7 9.6 - - + +
284K ILE* 4.2 18.2 - - + -
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Residues in contact with VAL 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I LYS* 5.3 1.6 + - - -
145K MET* 5.2 0.2 - - + -
146K LEU* 3.1 23.7 + - + +
147K LEU 4.3 8.7 - - - +
148K ALA 4.9 1.0 - - - -
149K LEU* 1.3 77.3 - - + +
151K PRO* 1.3 78.3 - - + +
154K GLY* 4.5 9.0 - - - -
155K HIS 4.7 2.2 - - - +
156K ILE* 4.1 25.1 - - + -
174K LEU* 5.9 2.5 - - + -
177K MET* 4.6 4.2 - - - +
179K ILE* 3.6 37.3 - - + +
202K ASN* 4.5 8.3 - - + +
203K LEU* 4.1 21.1 - - + -
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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