Contacts of the helix formed by residues 152 - 169 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.0 0.9 - - - -
150A GLY 3.6 3.1 + - - -
151A ARG* 1.3 72.8 - - - +
153A VAL* 1.3 62.3 + - - +
154A ASP* 3.3 12.0 + - - +
155A GLU* 3.1 42.4 + - - +
156A THR* 2.7 27.4 + - - -
158A ARG* 5.0 0.7 + - - -
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA* 3.9 29.4 - - + +
59A PHE* 3.6 33.2 - - + -
62A ARG* 3.5 41.7 - - + +
66A PHE* 3.9 22.4 - - + -
151A ARG 3.6 2.1 + - - +
152A SER* 1.3 72.3 + - - +
154A ASP* 1.3 64.4 + - - +
156A THR* 3.1 2.3 + - - -
157A LEU* 2.9 27.2 + - + +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.2 31.0 + - - -
152A SER* 3.3 7.9 + - - +
153A VAL* 1.3 78.6 - - - +
155A GLU* 1.3 62.7 + - - +
157A LEU* 3.3 9.0 + - - +
158A ARG* 3.1 47.6 + - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 4.5 14.7 + - - +
152A SER* 3.1 27.5 + - - +
154A ASP* 1.3 79.9 - - - +
156A THR* 1.3 59.9 + - - +
158A ARG* 3.4 18.9 + - - +
159A LEU* 3.0 27.0 + - - +
155B GLU* 3.1 45.4 - - - +
158B ARG* 4.1 9.9 + - - -
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.1 21.1 - - + -
59A PHE* 3.6 21.3 - - + -
66A PHE* 4.0 11.4 - - + -
130A LEU* 4.9 4.7 - - + -
132A ILE* 4.9 7.6 - - + -
151A ARG* 2.9 30.7 + - - +
152A SER 2.7 21.1 + - - -
153A VAL 3.1 4.3 + - - -
155A GLU* 1.3 74.4 - - - +
157A LEU* 1.3 68.5 + - - +
159A LEU* 3.1 8.6 + - + +
160A VAL* 3.0 23.2 + - + +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.6 15.7 - - - +
65A GLU* 3.5 44.2 - - + +
66A PHE* 3.5 42.0 - - + -
69A LEU* 4.1 11.7 - - + +
153A VAL* 2.9 22.2 + - + +
154A ASP* 3.7 9.0 - - - +
156A THR* 1.3 78.1 - - - +
158A ARG* 1.3 61.7 + - + +
160A VAL* 3.4 3.4 + - - +
161A GLN* 3.0 32.1 + - - +
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER* 5.0 1.0 + - - -
154A ASP* 3.1 41.3 + - - +
155A GLU* 3.6 33.7 + - - +
156A THR 3.2 0.2 - - - -
157A LEU* 1.3 76.8 - - + +
159A LEU* 1.3 57.5 + - - +
161A GLN* 3.4 16.1 + - - +
162A ALA* 2.8 30.0 + - - +
155B GLU* 3.8 11.8 + - - +
158B ARG* 5.0 8.1 - - - +
26C PHE* 5.6 15.9 - - + -
28C ASP* 5.8 4.2 + - - -
81C HIS* 6.4 0.2 - - - +
82C PHE* 5.3 1.4 - - - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.6 7.2 - - + -
132A ILE* 3.9 25.4 - - + -
141A GLN* 3.5 33.9 - - - +
151A ARG* 5.2 4.0 - - - +
155A GLU 3.0 13.5 + - - +
156A THR* 3.2 13.7 - - - +
158A ARG* 1.3 77.9 - - - +
160A VAL* 1.3 63.0 + - - +
162A ALA* 3.1 7.0 + - + +
163A PHE* 3.0 52.8 + - + -
145B ASN* 5.1 0.7 - - - +
147B LEU* 3.7 17.7 - - + -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 4.3 10.5 - - + -
40A VAL* 3.7 30.3 - - + -
66A PHE* 4.6 4.3 - - + -
69A LEU* 4.2 14.1 - - + -
71A CYS* 4.2 17.0 - - + -
132A ILE* 4.5 14.1 - - + -
156A THR 3.0 13.5 + - - +
157A LEU* 3.7 7.2 - - - +
159A LEU* 1.3 78.0 - - - +
161A GLN* 1.3 58.1 + - - +
163A PHE* 3.3 8.9 + - - +
164A GLN* 2.9 50.6 + - - +
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Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.8 32.0 - - + +
157A LEU* 3.0 20.5 + - - +
158A ARG* 3.7 18.8 + - - +
159A LEU 3.2 0.2 - - - -
160A VAL* 1.3 76.1 - - - +
162A ALA* 1.4 57.9 + - - +
164A GLN* 3.8 8.8 - - - +
165A PHE* 2.8 31.9 + - - +
81C HIS* 4.7 10.1 + - - -
82C PHE* 3.6 34.5 - - + -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ARG 2.8 18.3 + - - +
159A LEU* 3.1 10.7 + - - +
161A GLN* 1.4 69.9 - - - +
163A PHE* 1.3 66.2 + - - +
165A PHE* 3.7 5.5 - - - +
166A THR* 2.9 28.9 + - - -
147B LEU* 3.7 21.9 - - + +
149B VAL* 4.6 13.1 - - + +
26C PHE* 6.4 1.3 - - + -
82C PHE* 4.5 6.7 - - + -
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.3 21.3 - + + +
132A ILE* 4.1 20.2 - - + -
140A ARG* 3.4 56.8 - - + -
141A GLN* 3.7 13.5 - - + -
159A LEU* 3.0 50.5 + - + -
160A VAL* 3.6 6.7 - - - +
162A ALA* 1.3 75.1 - - - +
164A GLN* 1.3 59.6 + - - +
166A THR* 3.2 2.4 - - - +
167A ASP* 2.8 34.3 + - - +
145B ASN* 4.1 0.9 - - + -
146B ASP* 3.9 10.8 - - - -
147B LEU* 3.7 32.3 - - + +
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.5 38.4 - - + +
69A LEU* 2.8 43.9 + - - +
70A ASN 4.6 1.6 + - - -
160A VAL* 2.9 28.5 + - - +
161A GLN* 3.8 9.3 - - - +
163A PHE* 1.3 73.5 - - - +
165A PHE* 1.3 65.9 + - - +
167A ASP* 3.3 16.3 + - - +
168A LYS* 3.4 17.3 + - - +
25E GLN* 4.3 19.3 - - - +
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLN 2.8 20.7 + - - +
162A ALA* 3.7 4.5 - - - +
164A GLN* 1.3 71.8 - - - +
166A THR* 1.3 63.8 + - - +
168A LYS 3.2 0.9 + - - -
169A HIS* 2.8 75.5 + + + +
170A GLY 4.9 1.8 - - - -
172A VAL* 3.9 21.3 - - + -
149B VAL* 6.3 0.4 - - + -
82C PHE* 3.4 49.6 - + + -
85C LEU* 3.6 26.0 - - + -
86C ALA* 4.1 19.3 - - + -
89C ASN* 5.3 5.8 - - - -
82E PHE* 4.0 10.1 - + - -
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 5.0 2.5 - - - +
162A ALA 2.9 20.0 + - - +
163A PHE* 3.2 12.6 - - + +
165A PHE* 1.3 76.8 - - - +
167A ASP* 1.3 62.8 + - - +
169A HIS 2.3 27.4 - - - +
170A GLY* 3.1 23.1 + - - -
172A VAL* 4.1 5.2 - - - +
147B LEU* 3.7 8.7 - - + -
148B PRO* 3.5 37.6 + - + +
149B VAL* 3.8 13.9 - - - +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 2.6 32.1 + - - -
134A ASP* 4.5 2.7 - - - +
135A ASP* 4.2 6.2 - - - +
140A ARG* 2.8 29.4 + - - -
163A PHE 2.8 26.2 + - - +
164A GLN* 3.6 7.1 - - - +
165A PHE 3.3 0.4 - - - -
166A THR* 1.3 75.1 - - - +
168A LYS* 1.3 80.8 + - - +
169A HIS 5.0 0.2 - - - -
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASP* 5.2 9.7 + - - -
136A LYS* 5.4 7.9 - - - +
164A GLN 3.4 12.1 + - - +
165A PHE 3.2 1.4 + - - -
166A THR 3.1 0.2 - - - -
167A ASP* 1.3 99.5 + - - +
169A HIS* 1.3 81.6 + - + +
25E GLN* 5.9 4.5 - - - +
26E PHE* 4.2 35.0 - - + +
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Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 2.8 60.4 + + + +
166A THR 2.3 30.2 - - - +
168A LYS* 1.3 91.6 + - + +
170A GLY* 1.3 55.6 + - - +
86C ALA* 5.0 1.8 - - + +
89C ASN* 6.1 1.8 - - - +
201D CPS 3.8 17.6 + - - +
26E PHE* 4.7 6.3 - - - -
81E HIS* 3.3 37.8 - + - -
82E PHE* 3.3 21.2 - + - -
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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