Contacts of the helix formed by residues 179 - 193 (chain D) in PDB entry 5ID3
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 GLU 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D SER* 3.6 2.3 - - - -
178D ARG* 1.4 94.8 + - + +
180D LYS* 1.3 71.1 + - - +
181D LYS* 3.6 2.9 - - - +
182D LEU* 3.4 39.0 - - + +
183D LEU* 3.9 29.0 + - - +
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Residues in contact with LYS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ARG* 3.7 25.7 - - + +
179D GLU* 1.3 84.8 + - - +
181D LYS* 1.4 64.5 + - - +
183D LEU* 3.4 16.6 + - + +
184D LEU* 3.4 13.1 + - + +
312D ARG* 5.5 4.2 - - - +
311E LYS* 3.4 22.1 + - - +
314E ARG* 2.9 34.7 - - - +
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Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 4.6 8.5 + - - +
177D SER* 3.3 42.0 - - - +
178D ARG 5.9 0.2 - - - +
179D GLU 4.9 1.3 - - - +
180D LYS* 1.4 76.3 - - - +
182D LEU* 1.4 83.7 + - + +
183D LEU 3.5 0.2 + - - -
184D LEU* 3.5 6.3 + - - +
185D GLN* 3.2 31.8 + - + +
307E ARG* 5.0 4.8 + - - +
308E ASN* 5.0 15.4 + - - +
311E LYS* 4.0 33.0 - - + +
312E ARG* 6.1 3.2 - - - +
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D SER* 6.1 5.2 - - - +
178D ARG 5.7 0.2 - - - +
179D GLU* 3.4 37.4 + - + +
180D LYS 3.4 0.6 - - - -
181D LYS* 1.4 93.1 - - + +
183D LEU* 1.4 65.0 + - + +
185D GLN* 3.3 14.3 + - - +
186D LEU* 2.9 39.5 + - + +
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D GLU* 3.9 30.7 - - - +
180D LYS* 3.5 13.0 - - + +
181D LYS 3.3 0.4 - - - -
182D LEU* 1.4 84.2 - - + +
184D LEU* 1.3 61.8 + - - +
186D LEU* 3.1 14.9 - - + +
187D GLU* 3.1 19.4 + - + +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LYS* 3.4 9.5 + - + +
181D LYS 3.6 7.9 - - - +
182D LEU 3.3 0.2 - - - -
183D LEU* 1.3 78.5 - - - +
185D GLN* 1.4 59.2 + - - +
187D GLU* 3.0 44.7 + - - +
188D ASN* 3.4 4.7 + - - +
302D GLU* 5.2 0.9 - - - +
305D GLU* 4.5 6.7 - - + +
308D ASN* 5.9 1.1 - - + +
309D GLN* 3.6 31.2 - - + +
307E ARG* 3.4 44.5 + - - +
311E LYS* 3.6 24.2 - - + +
314E ARG* 4.1 5.4 - - - +
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Residues in contact with GLN 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D LYS* 3.2 24.2 + - + +
182D LEU* 3.3 16.6 + - - +
184D LEU* 1.4 74.4 - - - +
186D LEU* 1.4 61.5 + - - +
188D ASN* 3.2 18.2 + - + +
189D ALA* 3.3 10.7 + - - +
307E ARG* 4.3 10.4 - - - +
308E ASN* 4.3 24.3 + - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LEU* 2.9 23.1 + - + +
183D LEU* 3.1 19.7 - - + +
185D GLN* 1.4 77.8 - - - +
187D GLU* 1.4 59.6 + - - +
189D ALA* 3.1 23.0 + - + +
190D GLU* 3.2 31.6 + - + +
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Residues in contact with GLU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D LEU* 3.1 9.5 + - + +
184D LEU* 3.0 27.6 + - - +
186D LEU* 1.4 74.2 - - - +
188D ASN* 1.4 60.7 + - - +
190D GLU* 3.3 18.8 + - + +
191D THR* 3.0 27.7 + - - +
302D GLU* 4.8 0.4 - - - -
305D GLU* 2.7 47.4 - - + +
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU 3.4 4.1 + - - +
185D GLN* 3.2 16.8 + - + +
187D GLU* 1.4 78.8 - - - +
189D ALA* 1.4 62.9 + - - +
191D THR* 3.2 13.5 + - - -
192D LEU* 3.2 37.4 + - - +
299D LEU* 4.7 0.8 - - - +
302D GLU* 2.9 44.8 + - - +
304E ASP* 2.6 40.4 + - - +
307E ARG* 5.1 0.9 - - - +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D GLN 3.3 7.1 + - - +
186D LEU* 3.1 22.2 + - + +
188D ASN* 1.4 80.8 + - - +
190D GLU* 1.4 61.6 + - - +
192D LEU* 3.5 16.4 + - - +
193D LEU* 3.5 9.5 + - - -
194D ALA* 4.6 5.2 + - - +
195D PRO* 5.4 3.3 - - - +
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LEU* 3.2 33.9 + - + +
187D GLU* 3.5 18.5 - - + +
189D ALA* 1.4 76.0 - - + +
191D THR* 1.4 61.2 + - - +
193D LEU* 3.1 31.4 + - + +
195D PRO* 6.5 0.9 - - - -
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLU* 3.0 20.5 + - - +
188D ASN* 3.2 13.2 + - - -
190D GLU* 1.4 72.9 - - - +
192D LEU* 1.4 66.1 + - + +
193D LEU* 3.4 7.7 + - - +
298D ARG* 2.9 57.5 - - + +
299D LEU* 4.2 4.7 - - - +
301D THR* 4.5 5.2 - - - -
302D GLU* 4.4 17.9 + - + +
305D GLU* 5.6 2.6 + - - +
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Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ASN* 3.2 46.1 + - - +
189D ALA* 3.7 13.0 - - - +
190D GLU 3.4 0.4 - - - -
191D THR* 1.4 77.1 - - + +
193D LEU* 1.4 69.8 + - - +
194D ALA* 4.9 4.9 - - + +
294D GLU* 4.2 6.6 - - - +
295D LYS* 5.5 15.1 - - + +
298D ARG* 5.7 0.4 - - - -
299D LEU* 4.1 30.5 - - + +
301E THR* 5.2 12.1 - - + -
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ALA 3.5 3.7 + - - -
190D GLU* 3.1 27.7 + - + +
191D THR 3.2 11.3 - - - +
192D LEU* 1.4 82.0 - - - +
194D ALA* 1.4 59.9 + - - +
195D PRO* 4.8 2.2 - - - -
196D LEU* 4.1 23.6 - - + +
197D HIS* 3.3 23.3 + - - +
287D GLN* 3.6 22.7 - - - +
294D GLU* 3.4 29.3 - - + +
298D ARG* 3.0 35.2 - - + +
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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
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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