Contacts of the helix formed by residues 185 - 195 (chain D) in PDB entry 2P4K
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 ASN 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D THR 3.4 14.4 + - - +
80D ASN 2.7 26.3 + - - +
81D LEU 3.7 10.7 + - - -
82D SER* 3.8 20.0 - - - -
85D GLY* 4.7 2.0 - - - -
183D VAL 3.3 1.4 + - - -
184D ILE* 1.3 71.1 - - - +
186D TRP* 1.3 61.4 + - - +
187D GLU* 3.1 19.7 + - - +
188D ASN* 3.1 28.1 + - - +
189D VAL* 3.1 13.7 + - - +
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Residues in contact with TRP 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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85D GLY* 5.4 0.6 - - - -
86D GLY 3.5 23.9 - - - +
87D GLY 3.2 19.3 + - - -
88D GLU 4.1 6.1 - - - +
89D PRO* 3.7 39.7 - - + -
93D LEU* 4.0 7.6 - - + -
97D ILE* 4.4 5.4 - - + -
104D PHE* 3.6 22.2 - + - -
107D PHE* 3.7 23.6 - + - -
126D LEU* 4.9 2.7 - - + -
156D LEU* 4.0 12.1 - - + -
181D TRP* 4.1 14.8 + + - -
184D ILE* 3.1 30.4 + - + +
185D ASN* 1.3 72.9 + - - +
187D GLU* 1.3 56.8 + - - +
189D VAL* 3.6 31.9 - - + +
190D THR* 2.8 36.1 + - - -
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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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185D ASN* 3.1 14.5 + - - +
186D TRP* 1.3 79.2 - - - +
188D ASN* 1.3 62.4 + - - +
190D THR* 3.4 6.5 + - - -
191D GLU* 3.0 43.7 + - + +
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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
----------------------------------------------------------
79D THR* 3.1 41.1 + - - +
80D ASN* 3.0 17.5 + - - -
185D ASN* 3.1 21.5 + - - +
187D GLU* 1.3 76.0 - - - +
189D VAL* 1.3 65.1 + - - +
191D GLU* 3.1 22.4 + - - +
192D ARG* 2.9 51.5 + - - +
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ASN* 4.1 8.7 - - + +
93D LEU* 3.7 18.6 - - + -
126D LEU* 4.6 3.8 - - + -
155D LEU* 3.6 41.0 - - + +
156D LEU* 4.0 21.8 - - + -
184D ILE* 4.3 3.8 - - + -
185D ASN 3.1 14.5 + - - +
186D TRP* 3.2 29.4 + - + +
188D ASN* 1.3 76.1 - - - +
190D THR* 1.3 57.6 + - - +
192D ARG* 3.3 3.5 + - - +
193D TYR* 3.0 25.8 + - - +
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Residues in contact with THR 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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89D PRO* 4.4 6.2 - - - +
90D LYS 4.8 7.8 + - - +
93D LEU* 3.6 28.9 - - + +
186D TRP* 2.8 23.7 + - - +
187D GLU* 3.6 7.6 - - - +
189D VAL* 1.3 73.1 - - - +
191D GLU* 1.3 66.0 + - - +
193D TYR* 3.1 3.9 + - - +
194D MET* 2.8 42.2 + - + +
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Residues in contact with GLU 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 43.8 + - + +
188D ASN* 3.6 22.6 + - - +
190D THR* 1.3 76.7 - - + +
192D ARG* 1.3 64.6 + - + +
194D MET* 3.3 6.4 + - - +
195D ALA* 3.0 24.8 + - - +
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Residues in contact with ARG 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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76D ILE* 3.8 35.3 - - - +
79D THR* 2.8 29.1 + - - +
80D ASN* 3.7 4.4 - - - +
153D ILE* 5.1 2.6 - - + +
154D PRO* 3.8 15.6 + - - +
155D LEU* 3.4 36.9 - - + +
188D ASN* 2.9 35.8 + - - +
189D VAL 3.6 6.3 - - - +
191D GLU* 1.3 78.0 - - + +
193D TYR* 1.3 61.2 + - - +
195D ALA* 3.3 14.0 + - - +
196D CYS* 3.4 17.2 + - - -
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Residues in contact with TYR 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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92D GLU* 4.0 16.6 + - + +
93D LEU* 3.9 44.4 - - + -
96D ALA* 3.6 28.5 - - + +
99D ARG* 4.6 5.4 + - - -
128D PHE* 4.1 17.3 - + - -
135D LEU* 4.1 13.2 - - + -
155D LEU* 3.5 14.3 - - + +
189D VAL 3.0 14.3 + - - +
190D THR* 3.5 7.2 - - - +
192D ARG* 1.3 74.3 - - - +
194D MET* 1.3 73.6 + - + +
196D CYS* 2.8 26.5 - - - +
197D LYS* 3.0 46.9 + - + +
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Residues in contact with MET 194 (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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92D GLU* 3.9 35.9 - - + +
93D LEU 5.6 0.2 - - - -
190D THR* 2.8 33.7 + - + +
191D GLU* 3.9 6.3 - - - +
193D TYR* 1.3 92.1 - - + +
195D ALA* 1.3 57.4 + - - +
196D CYS 3.1 0.7 - - - -
197D LYS* 2.6 37.4 - - + +
198D LYS* 3.3 2.4 + - - +
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Residues in contact with ALA 195 (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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191D GLU 3.0 17.1 + - - +
192D ARG* 3.3 9.2 + - - +
193D TYR 3.1 0.8 - - - -
194D MET* 1.3 78.2 - - - +
196D CYS* 1.3 54.7 + - - +
198D LYS* 3.2 28.7 - - + +
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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