Contacts of the helix formed by residues 162 - 175 (chain D) in PDB entry 2X4O
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 GLY 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D ALA 3.2 14.7 + - - -
159D TYR 3.3 1.2 + - - -
161D GLU* 1.3 78.9 - - - +
163D THR* 1.3 56.4 + - - +
164D CYS 3.1 0.9 + - - -
165D VAL* 3.2 4.0 + - - +
166D GLU* 2.7 39.4 + - - +
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Residues in contact with THR 163 (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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66D LYS* 5.8 0.7 - - - +
158D ALA 4.2 1.6 + - - -
159D TYR* 3.3 34.4 + - + -
162D GLY* 1.3 69.6 - - - -
164D CYS* 1.3 65.2 + - - +
166D GLU* 4.1 13.7 + - - -
167D TRP* 2.9 39.2 + - + +
1F LYS* 4.1 16.4 - - + -
2F LEU 4.8 2.9 - - - +
4F PRO* 5.7 6.3 - - + +
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Residues in contact with CYS 164 (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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5D MET* 3.3 30.2 - - - +
100D GLY* 3.7 10.3 - - - -
101D CYS* 2.0 52.5 - - - -
159D TYR* 2.8 45.6 + - + +
160D LEU* 3.4 8.1 - - - +
163D THR* 1.3 74.0 - - - +
165D VAL* 1.3 56.5 + - - +
168D LEU* 3.1 24.3 + - - +
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Residues in contact with VAL 165 (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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101D CYS* 3.7 17.0 - - + -
102D ASP 4.4 1.1 - - - +
103D VAL* 3.9 18.2 - - + -
109D PHE* 3.7 25.8 - - + -
160D LEU 3.4 14.3 + - - +
161D GLU* 3.3 26.7 - - - +
162D GLY* 3.2 2.4 + - - +
164D CYS* 1.3 73.3 - - - +
166D GLU* 1.3 69.6 + - - +
168D LEU* 3.7 5.0 - - - +
169D ARG* 3.1 52.8 + - - +
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Residues in contact with GLU 166 (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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162D GLY 2.7 22.3 + - - +
163D THR* 3.6 16.1 + - - +
165D VAL* 1.3 76.2 - - - +
167D TRP* 1.3 83.7 + - + +
169D ARG* 3.4 18.6 + - - +
170D ARG* 3.2 23.6 + - + +
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Residues in contact with TRP 167 (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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55D GLU* 3.8 15.9 - - + -
59D TYR* 4.2 13.2 - + + -
163D THR* 2.9 29.1 + - + +
164D CYS 4.4 1.6 - - - +
166D GLU* 1.3 96.8 + - - +
168D LEU* 1.3 67.9 + - - +
169D ARG 3.2 1.6 - - - -
170D ARG* 3.1 52.3 + - + +
171D TYR* 2.8 52.8 + + + -
1F LYS* 3.4 63.3 - - + +
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Residues in contact with LEU 168 (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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3D HIS* 3.9 11.7 - - + +
4D SER 3.8 10.5 - - - +
5D MET* 3.8 19.6 - - + +
28D VAL* 3.8 23.6 - - + -
101D CYS* 3.8 26.2 - - - +
103D VAL* 3.9 23.3 - - + -
164D CYS 3.1 19.3 + - - +
165D VAL* 3.7 6.1 - - - +
167D TRP* 1.3 75.0 - - - +
169D ARG* 1.3 57.9 + - - +
171D TYR* 3.2 8.4 + - - +
172D LEU* 3.0 55.1 + - + +
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Residues in contact with ARG 169 (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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103D VAL* 4.5 7.5 - - + +
107D TRP* 2.9 58.7 + - + +
108D ARG* 4.6 4.9 - - - +
109D PHE 4.7 1.6 - - - +
165D VAL* 3.1 47.5 + - - +
166D GLU* 3.6 16.7 + - - +
168D LEU* 1.3 74.5 - - - +
170D ARG* 1.3 62.2 + - - +
172D LEU* 3.4 10.6 + - + +
173D GLU* 3.1 33.3 + - - +
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Residues in contact with ARG 170 (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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55D GLU* 4.2 7.9 + - - -
166D GLU* 3.2 15.8 + - - +
167D TRP* 3.1 58.5 + - + +
169D ARG* 1.3 79.2 - - - +
171D TYR* 1.3 56.3 + - + +
173D GLU* 3.4 14.5 + - - +
174D ASN* 3.0 47.5 + - - +
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Residues in contact with TYR 171 (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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5D MET* 3.5 33.7 - - - -
28D VAL* 3.9 17.7 - - + -
33D PHE* 3.7 12.0 - + - -
51D TRP* 3.7 19.3 - + + -
52D ILE* 3.7 26.2 - - + -
55D GLU* 4.5 1.6 - - - -
59D TYR* 2.9 30.5 + + - -
167D TRP* 2.8 44.3 + + - +
168D LEU* 3.7 4.0 - - - +
170D ARG* 1.3 71.5 - - - +
172D LEU* 1.3 62.1 + - - +
174D ASN* 3.8 8.0 - - - +
175D GLY 2.8 28.1 + - - -
179D LEU* 3.5 8.4 - - - +
1F LYS* 2.8 25.3 + - - +
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Residues in contact with LEU 172 (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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3D HIS* 3.7 42.4 - - + +
28D VAL* 3.9 21.8 - - + -
29D ASP* 4.4 0.2 - - - +
103D VAL* 4.7 4.3 - - + -
107D TRP* 3.6 33.0 - - + +
168D LEU* 3.0 42.4 + - + +
169D ARG* 3.7 6.1 - - - +
170D ARG 3.4 0.2 - - - -
171D TYR* 1.3 76.6 - - - +
173D GLU* 1.3 57.7 + - - +
176D LYS* 3.0 19.4 + - - -
179D LEU* 4.2 16.4 - - + -
180D GLN* 2.9 22.0 + - + +
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Residues in contact with GLU 173 (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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107D TRP* 3.9 19.7 - - + -
169D ARG* 3.1 20.9 + - - +
170D ARG* 3.5 17.5 - - - +
171D TYR 3.1 0.6 - - - -
172D LEU* 1.3 75.4 - - - +
174D ASN* 1.3 68.2 + - - +
176D LYS* 3.4 33.8 - - - +
180D GLN* 4.5 1.3 - - - +
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Residues in contact with ASN 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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51D TRP* 3.9 23.3 - - + +
52D ILE* 5.3 0.4 - - - +
55D GLU* 2.9 38.8 + - - -
170D ARG* 3.0 30.8 + - - +
171D TYR* 3.8 9.5 - - - +
173D GLU* 1.3 80.7 - - - +
175D GLY* 1.3 59.5 + - - +
176D LYS* 3.6 2.9 + - - +
177D GLU 5.2 0.5 + - - -
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Residues in contact with GLY 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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51D TRP* 3.4 30.2 - - - +
171D TYR 2.8 16.1 + - - -
172D LEU 3.8 2.5 - - - -
174D ASN* 1.3 72.4 - - - +
176D LYS* 1.3 50.9 + - - +
177D GLU* 3.0 6.3 - - - -
178D THR* 2.8 9.1 + - - -
179D LEU* 2.7 37.9 + - - +
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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