Contacts of the helix formed by residues 173 - 186 (chain D) in PDB entry 1APL
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 ARG 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A A 4.4 10.5 + - - -
162D LEU* 3.9 29.9 - - + +
166D MET* 4.2 18.4 - - - -
171D LEU 3.8 0.8 + - - -
172D SER* 1.3 66.1 - - - +
174D ILE* 1.3 72.7 + - + +
176D ILE* 3.0 18.9 + - - +
177D LYS* 2.8 88.4 + - - +
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Residues in contact with ILE 174 (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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39B C 5.4 7.9 - - - +
172D SER 2.6 6.2 + - - +
173D ARG* 1.3 97.2 - - + +
175D GLN* 1.3 52.6 + - + +
177D LYS* 2.7 13.4 + - + +
178D ASN* 2.7 53.3 + - - +
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Residues in contact with GLN 175 (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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38B A 3.0 43.0 + - - +
136D PHE* 3.6 24.3 - - + -
171D LEU* 4.0 17.7 - - + +
172D SER* 2.8 45.9 + - - +
174D ILE* 1.3 75.7 - - + +
176D ILE* 1.3 64.5 + - - +
178D ASN* 3.7 3.9 + - - +
179D TRP* 2.9 24.6 + - - +
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Residues in contact with ILE 176 (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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144D LEU* 3.7 20.2 - - + -
157D LEU* 3.5 23.1 - - + -
162D LEU* 5.5 4.3 - - + -
165D LEU* 3.9 19.3 - - + -
166D MET* 4.7 12.8 - - + +
169D THR* 4.0 14.4 - - + -
171D LEU* 3.4 37.7 - - + +
173D ARG* 3.0 32.9 + - - +
175D GLN* 1.3 77.0 - - - +
177D LYS* 1.3 66.5 + - - +
179D TRP* 3.2 5.5 + - - +
180D VAL* 3.0 26.6 + - + +
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Residues in contact with LYS 177 (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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1A A 4.2 23.1 + - - +
2A C 4.4 14.2 + - - +
157D LEU* 4.1 26.8 + - - +
162D LEU* 3.5 19.9 - - - +
173D ARG* 2.8 49.9 + - - +
174D ILE* 2.7 24.5 + - + +
176D ILE* 1.3 78.9 - - - +
178D ASN* 1.3 55.5 + - - +
180D VAL* 3.0 15.8 + - - +
181D SER* 3.1 13.1 + - - -
184D ARG* 5.1 3.9 + - - +
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Residues in contact with ASN 178 (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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37B T 5.9 0.9 - - + -
38B A 4.3 23.9 + - + +
39B C 3.9 32.7 + - - -
40B A 5.7 0.2 + - - -
174D ILE* 2.7 40.7 + - - +
175D GLN* 4.1 4.8 - - - +
177D LYS* 1.3 71.4 - - - +
179D TRP* 1.4 64.1 + - - +
181D SER* 4.4 7.8 - - - +
182D ASN* 2.9 40.7 + - - +
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Residues in contact with TRP 179 (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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37B T 3.7 17.3 + - + -
136D PHE* 3.7 30.3 - + + -
141D VAL* 4.9 10.7 - - + +
144D LEU* 3.6 61.2 - - + +
145D GLU* 3.5 24.7 - - + -
147D TRP* 5.7 1.1 - + - -
148D PHE* 4.3 6.7 - + + -
175D GLN 2.9 20.3 + - - +
176D ILE* 3.2 5.3 + - - +
178D ASN* 1.4 73.8 - - - +
180D VAL* 1.3 65.2 + - + +
182D ASN* 3.9 4.5 - - + +
183D ARG* 2.9 70.4 + - + +
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Residues in contact with VAL 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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144D LEU* 4.8 0.9 - - + -
147D TRP* 3.5 28.9 - - + -
148D PHE* 4.0 13.0 - - + -
155D PRO 3.9 15.7 - - - +
156D TYR* 5.4 0.2 - - - -
157D LEU* 3.8 30.3 - - + -
165D LEU* 5.2 0.2 - - + -
176D ILE* 3.1 21.3 - - + +
177D LYS 3.0 5.8 + - - +
179D TRP* 1.3 87.0 - - + +
181D SER* 1.3 55.3 + - - +
183D ARG* 3.0 2.6 + - - +
184D ARG* 2.8 38.8 + - - +
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Residues in contact with SER 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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2A C 6.0 0.2 - - - -
3A A 4.4 8.0 + - - -
4A T 3.9 24.8 + - - +
177D LYS 3.1 12.4 + - - -
178D ASN* 3.9 11.9 - - - -
180D VAL* 1.3 70.2 - - - +
182D ASN* 1.3 63.0 + - - +
184D ARG* 3.2 32.5 + - - +
185D ARG* 2.9 25.3 + - - +
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Residues in contact with ASN 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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4A T 5.0 0.3 - - - +
37B T 3.9 26.7 - - + +
38B A 3.1 34.6 + - - +
39B C 4.1 5.3 + - - -
178D ASN* 2.9 27.1 + - - +
179D TRP* 4.1 4.3 - - + +
181D SER* 1.3 80.7 + - - +
183D ARG* 1.4 57.8 + - - +
185D ARG* 2.5 56.1 + - - +
186D LYS* 3.0 13.0 + - - +
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Residues in contact with ARG 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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145D GLU* 2.8 39.3 + - - +
148D PHE* 3.3 38.1 - - + -
179D TRP* 2.9 54.2 + - + +
180D VAL* 3.0 5.1 + - - +
182D ASN* 1.4 74.9 - - - +
184D ARG* 1.3 60.8 + - - +
186D LYS* 3.4 42.0 + - - +
187D GLU* 2.7 42.3 + - - +
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Residues in contact with ARG 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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2A C 3.4 24.5 + - - -
3A A 2.5 45.7 + - - +
148D PHE* 4.2 11.0 - - + -
155D PRO* 3.2 38.7 + - + +
156D TYR* 3.6 37.2 - - - +
157D LEU* 4.8 3.4 - - - +
177D LYS* 5.1 4.0 + - - +
180D VAL* 2.8 22.6 + - - +
181D SER* 3.3 33.8 - - - +
182D ASN 3.1 0.2 - - - -
183D ARG* 1.3 74.3 - - - +
185D ARG* 1.3 65.3 + - - +
187D GLU* 3.0 18.9 + - - +
188D LYS 4.3 0.2 + - - -
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Residues in contact with ARG 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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4A T 3.0 48.7 - - + +
5A G 3.0 22.5 + - - -
6A T 4.0 12.1 + - - +
37B T 4.9 3.8 - - - +
38B A 3.3 15.2 - - - +
181D SER 2.9 11.3 + - - +
182D ASN* 2.5 44.9 + - - +
184D ARG* 1.3 77.9 - - - +
186D LYS* 1.3 58.7 + - - +
188D LYS* 2.9 31.6 + - + +
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Residues in contact with LYS 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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35B A 3.8 11.3 + - - +
36B T 2.9 42.5 + - - -
145D GLU* 5.9 0.7 - - - -
182D ASN 3.0 10.7 + - - +
183D ARG* 3.7 38.8 + - - +
184D ARG 3.3 0.4 - - - -
185D ARG* 1.3 78.4 - - - +
187D GLU* 1.3 56.0 + - - +
188D LYS* 3.1 6.5 + - - -
189D THR* 3.8 19.0 + - - +
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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
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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