Contacts of the helix formed by residues 152 - 170 (chain D) in PDB entry 4XCS
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 152 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PHE* 4.7 0.4 - - - -
150D GLY 3.7 2.0 + - - -
151D ARG* 1.3 70.6 - - - +
153D VAL* 1.3 62.4 + - - +
154D ASP* 3.3 9.9 + - - +
155D GLU* 2.9 44.7 + - - +
156D THR* 2.7 27.9 + - - -
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Residues in contact with VAL 153 (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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58D ALA* 3.7 41.5 - - + +
59D PHE* 3.8 25.8 - - + +
62D ARG* 3.5 39.7 - - + +
66D PHE* 3.8 16.2 - - + -
151D ARG 3.5 2.9 + - - +
152D SER* 1.3 72.9 + - - +
154D ASP* 1.3 64.3 + - - +
156D THR* 3.0 3.1 + - - -
157D LEU* 2.9 31.0 + - + +
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG* 2.8 40.9 + - - +
152D SER* 3.3 7.0 + - - +
153D VAL* 1.3 77.9 - - - +
155D GLU* 1.3 63.0 + - - +
157D LEU* 3.4 5.7 + - - +
158D ARG* 3.1 46.7 + - - +
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Residues in contact with GLU 155 (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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155C GLU* 3.5 33.6 - - - +
158C ARG* 3.2 28.4 + - - -
152D SER* 2.9 28.4 + - - +
154D ASP* 1.3 77.5 - - - +
156D THR* 1.3 64.0 + - - +
158D ARG* 3.2 29.1 + - - +
159D LEU* 3.0 24.4 + - - +
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Residues in contact with THR 156 (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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40D VAL* 4.0 23.6 - - + -
59D PHE* 3.5 31.7 - - + -
66D PHE* 4.1 7.4 - - + -
130D LEU* 4.6 17.7 - - + +
132D ILE* 4.7 6.7 - - + -
151D ARG* 4.7 5.7 - - - +
152D SER 2.7 21.3 + - - -
153D VAL 3.0 5.6 + - - -
155D GLU* 1.3 79.1 - - - +
157D LEU* 1.3 62.4 + - - +
159D LEU* 3.2 8.6 + - + +
160D VAL* 2.9 22.9 + - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG* 3.2 31.4 - - - +
65D GLU* 3.7 24.5 - - + +
66D PHE* 3.4 42.6 - - + -
69D LEU* 3.7 17.4 - - + +
153D VAL* 2.9 21.6 + - + +
154D ASP* 3.6 7.2 - - - +
156D THR* 1.3 76.8 - - - +
158D ARG* 1.3 62.5 + - + +
160D VAL* 3.2 4.6 + - - +
161D GLN* 2.9 34.6 + - - +
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Residues in contact with ARG 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLU* 4.8 5.5 + - - -
158C ARG* 4.9 6.1 - - - +
154D ASP* 3.1 36.9 + - - +
155D GLU* 3.2 36.8 + - - +
156D THR 3.3 0.2 - - - -
157D LEU* 1.3 80.5 - - + +
159D LEU* 1.3 58.2 + - - +
161D GLN* 3.3 16.3 + - - +
162D ALA* 2.8 29.5 + - - +
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Residues in contact with LEU 159 (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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145C ASN* 5.0 0.4 - - - +
147C LEU* 3.7 20.2 - - + -
130D LEU* 4.4 8.7 - - + -
132D ILE* 3.8 24.2 - - + -
141D GLN* 3.3 43.3 - - - +
155D GLU 3.0 15.1 + - - +
156D THR* 3.3 11.0 - - - +
158D ARG* 1.3 74.1 - - - +
160D VAL* 1.3 68.7 + - + +
162D ALA* 3.1 5.3 + - + +
163D PHE* 2.9 42.4 + - + -
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 4.3 13.0 - - + -
40D VAL* 3.7 30.1 - - + -
66D PHE* 4.3 5.4 - - + -
69D LEU* 4.2 13.7 - - + -
71D CYS* 4.2 14.1 - - + -
132D ILE* 4.4 13.7 - - + -
156D THR 2.9 15.7 + - - +
157D LEU 3.6 7.0 - - - +
159D LEU* 1.3 79.9 - - - +
161D GLN* 1.3 62.2 + - - +
163D PHE* 3.2 10.7 + - - +
164D GLN* 3.0 46.0 + - - +
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Residues in contact with GLN 161 (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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69D LEU* 3.9 34.1 - - + +
157D LEU* 2.9 26.9 + - - +
158D ARG* 3.5 20.8 + - - +
160D VAL* 1.3 75.1 - - - +
162D ALA* 1.3 58.1 + - - +
164D GLN* 3.2 8.2 + - - +
165D PHE* 2.8 32.9 + - - +
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Residues in contact with ALA 162 (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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147C LEU* 3.7 24.9 - - + -
149C VAL* 4.5 12.1 - - + -
158D ARG 2.8 16.9 + - - +
159D LEU* 3.1 7.2 + - + +
161D GLN* 1.3 77.0 - - - +
163D PHE* 1.3 58.8 + - - +
165D PHE* 3.9 4.8 - - - +
166D THR* 2.8 32.3 + - - +
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Residues in contact with PHE 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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145C ASN* 4.0 1.8 - - + -
146C ASP* 4.0 0.2 - - - -
147C LEU* 3.7 29.8 - - + -
38D TYR* 3.4 22.7 - + + +
132D ILE* 3.9 22.2 - - + -
140D ARG* 3.6 68.0 - - + -
141D GLN* 3.7 13.5 - - + -
159D LEU* 2.9 48.8 + - + -
160D VAL* 3.2 6.3 + - - +
162D ALA* 1.3 77.4 - - - +
164D GLN* 1.3 52.9 + - - +
166D THR* 3.0 4.5 + - - -
167D ASP* 2.8 39.3 + - - +
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Residues in contact with GLN 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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38D TYR* 3.5 40.2 - - + +
69D LEU* 2.8 46.2 + - - +
70D ASN* 4.5 3.6 + - - +
160D VAL* 3.0 27.9 + - - +
161D GLN* 3.2 6.8 + - - +
163D PHE* 1.3 72.6 - - - +
165D PHE* 1.3 67.3 + - - +
167D ASP* 3.1 10.3 + - - +
168D LYS* 3.0 23.9 + - - +
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Residues in contact with PHE 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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161D GLN 2.8 18.9 + - - +
162D ALA* 3.9 4.7 - - - +
164D GLN* 1.3 75.1 - - - +
166D THR* 1.3 61.4 + - + +
168D LYS* 3.1 4.7 + - - +
169D HIS* 2.8 70.6 + + + +
170D GLY 5.1 0.2 - - - -
172D VAL* 3.8 29.4 - - + -
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Residues in contact with THR 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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147C LEU* 3.7 6.2 - - - +
148C PRO* 3.7 22.3 - - + +
149C VAL* 3.7 26.2 - - + -
140D ARG* 4.5 5.0 + - - -
162D ALA* 2.8 23.2 + - - +
163D PHE* 3.0 12.1 + - - -
165D PHE* 1.3 72.7 - - + +
167D ASP* 1.3 61.9 + - - +
170D GLY* 2.8 45.7 + - - +
172D VAL* 3.8 12.1 - - + -
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Residues in contact with ASP 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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38D TYR* 2.5 33.3 + - - -
134D ASP* 4.4 4.4 - - - +
135D ASP* 4.3 5.5 - - - +
140D ARG* 2.5 32.4 + - - -
163D PHE 2.8 20.3 + - - +
164D GLN* 3.1 11.0 + - - +
166D THR* 1.3 74.5 + - - +
168D LYS* 1.3 59.6 - - + +
170D GLY 4.7 0.3 + - - -
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Residues in contact with LYS 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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164D GLN 3.0 11.2 + - - +
165D PHE* 3.6 7.4 - - - +
167D ASP* 1.3 78.6 - - + +
169D HIS* 1.3 93.6 + - + +
170D GLY 3.8 0.2 - - - -
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Residues in contact with HIS 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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165D PHE* 2.8 61.2 + + + +
168D LYS* 1.3 119.4 + - + +
170D GLY* 1.3 59.7 + - - +
171D GLU 4.9 1.7 - - - +
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Residues in contact with GLY 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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148C PRO* 4.6 2.2 - - - -
166D THR* 2.8 40.8 + - - +
167D ASP 4.7 0.4 + - - -
168D LYS 3.8 1.0 - - - -
169D HIS* 1.3 75.8 - - - +
171D GLU* 1.3 66.4 + - - +
172D VAL* 3.4 5.2 + - - +
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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
------------------------------------------------------------
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