Contacts of the helix formed by residues 151 - 170 (chain A) in PDB entry 4U1D
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 ILE 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 5.5 2.7 - - + +
107A GLU* 4.2 22.0 - - + +
108A GLN* 4.6 26.7 - - - +
111A ALA* 3.5 31.6 - - + -
114A LEU* 5.6 5.8 - - + -
150A ALA* 1.3 86.1 - - + +
152A THR* 1.3 59.6 + - - +
153A SER 3.3 0.7 - - - -
154A TRP* 3.1 10.0 + - + +
155A LEU* 3.0 36.4 + - + +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA* 4.5 10.6 - - - +
151A ILE* 1.3 80.0 - - - +
153A SER* 1.3 57.5 + - - +
155A LEU* 3.1 13.3 + - - +
156A ARG* 2.9 29.4 + - + +
195A ARG* 4.8 7.3 + - - +
441C THR* 6.6 0.4 - - - -
491C PHE 3.8 9.2 - - - +
492C ALA* 3.5 39.3 - - + +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.5 27.6 + - - -
150A ALA* 2.9 28.2 + - - +
152A THR* 1.3 78.5 - - - +
154A TRP* 1.3 58.7 + - - +
156A ARG* 3.8 7.4 - - - +
157A PHE* 2.9 26.2 + - - +
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Residues in contact with TRP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL 3.4 25.6 - - - -
61A GLU 4.2 7.4 - - - -
63A LYS* 3.6 37.1 - - + +
103A LYS* 3.7 35.4 - - + -
104A ILE* 3.7 14.8 - - + -
107A GLU* 3.5 41.0 + - + -
150A ALA 3.3 24.1 + - - -
151A ILE* 3.1 10.0 + - + +
152A THR 3.1 0.4 - - - -
153A SER* 1.3 81.7 + - - +
155A LEU* 1.3 58.9 + - - +
157A PHE* 3.3 22.2 + + - +
158A THR* 2.9 34.7 + - + +
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Residues in contact with LEU 155 (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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104A ILE* 3.6 21.1 - - + -
108A GLN* 5.3 2.5 - - - +
151A ILE* 3.0 23.0 + - + +
152A THR* 3.3 13.7 - - - +
154A TRP* 1.3 75.9 - - - +
156A ARG* 1.3 57.9 + - - +
158A THR* 2.8 17.4 + - - -
159A TRP* 3.0 14.0 + - - +
189A PHE* 3.6 18.0 - - + -
193A TYR* 3.5 46.9 - - + -
195A ARG* 3.6 28.7 - - - +
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A THR* 2.9 18.2 + - + +
153A SER* 3.8 9.2 - - - +
155A LEU* 1.3 76.2 - - - +
157A PHE* 1.3 57.8 + - - +
159A TRP* 3.4 13.0 + - - +
160A GLU* 3.0 59.5 + - - +
163A ARG* 3.8 5.7 - - - +
195A ARG* 3.5 8.9 - - - +
198A GLU* 3.0 26.7 + - - +
476C ASP* 2.8 48.1 + - - -
477C TYR 4.3 1.0 - - - -
478C VAL* 3.8 12.7 - - - +
479C SER* 3.6 33.9 - - - +
492C ALA 6.5 0.4 - - - -
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Residues in contact with PHE 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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60A VAL* 4.4 8.1 - - + -
63A LYS* 3.7 33.4 - - + -
65A GLY* 3.6 31.9 - - - -
68A LEU* 4.1 20.0 - - + -
100A VAL* 3.4 29.4 - - + -
103A LYS* 6.1 0.2 - - + -
153A SER 2.9 19.8 + - - +
154A TRP* 3.3 33.0 - + + +
155A LEU 3.2 0.2 - - - -
156A ARG* 1.3 76.5 - - - +
158A THR* 1.3 61.4 + - + +
160A GLU* 3.1 17.2 + - + +
161A SER* 2.9 39.2 + - - -
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Residues in contact with THR 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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100A VAL* 3.6 29.1 - - + +
101A GLU* 5.3 0.7 - - - -
103A LYS* 5.9 0.4 - - + -
104A ILE* 3.3 29.9 - - + +
154A TRP* 2.9 14.8 + - + +
155A LEU* 2.8 23.9 + - - -
157A PHE* 1.3 76.5 - - + +
159A TRP* 1.3 66.3 + - - +
161A SER* 3.1 7.8 + - - -
162A TYR* 2.9 37.9 + - - -
189A PHE* 3.6 16.0 - - - -
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Residues in contact with TRP 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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155A LEU 3.0 13.6 + - - +
156A ARG* 3.5 32.8 - - - +
157A PHE 3.3 0.2 - - - -
158A THR* 1.3 76.9 + - - +
160A GLU* 1.3 69.8 + - + +
161A SER 3.2 0.2 + - - -
162A TYR* 3.4 3.9 + - + +
163A ARG* 2.9 40.7 + - + +
166A LEU* 6.1 0.2 - - + -
186A THR* 3.7 29.4 - - + -
189A PHE* 4.0 15.6 - + + -
190A CYS* 4.3 5.6 - - - -
198A GLU* 3.2 63.3 - - + +
201A ARG* 4.6 10.3 - - + -
202A LEU* 3.9 16.4 - - + -
205A MET* 4.4 9.2 - - + -
476C ASP* 2.9 27.9 + - - -
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Residues in contact with GLU 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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65A GLY* 5.8 2.6 - - - -
156A ARG* 3.0 53.1 + - - +
157A PHE* 3.5 19.2 - - + +
159A TRP* 1.3 77.6 - - + +
161A SER* 1.3 57.0 + - - +
163A ARG* 3.3 35.5 + - - +
164A ALA* 2.9 29.3 + - - +
438C GLN* 5.5 5.4 + - - -
477C TYR 5.5 2.6 - - - +
478C VAL* 6.0 0.2 - - - -
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Residues in contact with SER 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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65A GLY* 5.7 1.0 - - - -
96A PHE* 3.3 33.4 - - - -
97A ILE* 4.6 0.7 - - - -
100A VAL* 3.7 23.5 - - - +
157A PHE* 2.9 22.0 + - - -
158A THR* 3.4 9.0 - - - -
159A TRP 3.1 0.2 - - - -
160A GLU* 1.3 73.7 - - - +
162A TYR* 1.3 65.5 + - - +
163A ARG 3.2 1.1 - - - -
164A ALA* 3.1 5.1 + - - +
165A VAL* 2.9 30.1 + - - +
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Residues in contact with TYR 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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97A ILE* 3.8 38.8 - - + +
100A VAL* 5.7 4.3 - - + -
101A GLU* 3.2 34.2 + - + +
158A THR* 2.9 33.0 + - - +
159A TRP* 3.7 5.6 - + + +
161A SER* 1.3 71.8 - - - +
163A ARG* 1.3 57.7 + - - +
165A VAL* 3.3 2.1 + - - +
166A LEU* 2.9 35.6 + - - +
182A VAL* 3.9 5.7 - - + +
185A LYS* 3.7 25.2 + - + +
186A THR* 3.4 31.0 - - + +
189A PHE* 3.7 42.3 - + + +
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Residues in contact with ARG 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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156A ARG* 3.8 3.0 - - - +
159A TRP* 2.9 35.5 + - + +
160A GLU* 3.3 39.8 + - - +
162A TYR* 1.3 77.5 - - - +
164A ALA* 1.3 57.6 + - - +
166A LEU* 3.3 8.5 + - - +
167A ASP* 2.9 27.9 + - + +
201A ARG* 5.4 3.8 - - - +
205A MET* 4.2 24.9 - - + +
340C ILE* 3.6 38.3 - - - +
341C PRO* 4.5 11.3 - - + +
476C ASP* 2.6 53.5 + - - +
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Residues in contact with ALA 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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69A LYS* 4.0 36.8 - - + -
73A HIS* 4.4 5.1 - - - -
96A PHE* 5.2 5.8 - - + -
160A GLU 2.9 19.6 + - - +
161A SER* 3.5 7.2 - - - +
163A ARG* 1.3 77.1 - - - +
165A VAL* 1.3 59.3 + - + +
167A ASP* 3.2 9.5 + - - +
168A LEU* 2.9 27.8 + - - +
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Residues in contact with VAL 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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72A LEU* 4.9 7.4 - - + -
93A ALA* 4.2 9.9 - - + +
96A PHE* 3.6 24.0 - - + -
97A ILE* 3.5 24.5 - - + -
161A SER 2.9 19.7 + - - +
162A TYR 3.7 3.6 - - - +
164A ALA* 1.3 77.3 - - - +
166A LEU* 1.3 56.7 + - - +
168A LEU* 2.9 9.5 + - + +
169A LEU* 2.9 43.8 + - + +
182A VAL* 3.8 30.5 - - + -
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Residues in contact with LEU 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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162A TYR 2.9 20.1 + - - +
163A ARG* 3.6 5.8 - - - +
165A VAL* 1.3 75.2 - - - +
167A ASP* 1.3 62.3 + - - +
169A LEU* 5.8 0.2 - - + -
170A ARG* 3.2 25.1 + - - +
179A TYR* 3.7 23.3 - - + -
182A VAL* 3.6 26.2 - - + -
183A VAL* 3.7 28.3 - - + +
186A THR* 3.7 17.5 - - + +
202A LEU* 3.6 31.2 - - + -
205A MET* 4.6 9.4 - - + -
206A LEU* 4.8 4.0 - - + -
209A HIS* 3.8 8.2 - - + -
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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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73A HIS* 3.9 17.9 + - + -
163A ARG 2.9 13.1 + - - +
164A ALA* 3.2 11.9 + - - +
166A LEU* 1.3 75.2 - - - +
168A LEU* 1.3 58.9 + - - +
170A ARG* 3.1 39.7 + - - +
205A MET* 5.4 2.0 - - - +
209A HIS* 4.3 7.0 + - - -
341C PRO* 3.8 40.8 - - + +
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Residues in contact with LEU 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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72A LEU* 3.8 37.7 - - + +
73A HIS* 3.8 38.8 - - + +
76A LYS* 3.5 47.5 - - + +
89A VAL* 4.9 10.1 - - + +
92A VAL* 6.0 0.4 - - + -
93A ALA* 4.8 6.7 - - + -
164A ALA 2.9 11.8 + - - +
165A VAL* 2.9 12.5 + - - +
167A ASP* 1.3 79.6 - - - +
169A LEU* 1.3 72.3 + - + +
170A ARG* 3.2 8.8 + - - +
172A ASN* 5.7 0.2 - - - +
175A LEU* 4.6 2.4 - - - +
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Residues in contact with LEU 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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89A VAL* 4.8 4.9 - - + -
90A GLY* 5.2 1.3 - - - -
93A ALA* 3.7 23.1 - - + -
165A VAL* 2.9 31.5 + - + +
168A LEU* 1.3 88.7 - - + +
170A ARG* 1.3 65.4 + - - +
171A ASN 3.5 1.4 + - - -
172A ASN* 3.8 15.2 + - - +
175A LEU* 4.1 29.5 - - + +
176A GLU* 5.7 0.2 - - - -
178A THR* 3.7 21.3 - - + +
179A TYR* 3.5 51.6 - - + +
182A VAL* 4.0 2.7 - - + -
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Residues in contact with ARG 170 (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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166A LEU 3.2 15.4 + - - +
167A ASP* 3.1 43.6 + - - +
168A LEU 3.2 4.1 - - - +
169A LEU* 1.3 79.0 - - - +
171A ASN* 1.3 95.7 + - - +
172A ASN* 3.3 3.5 + - - +
179A TYR* 4.2 8.1 - - - -
208A GLN* 6.0 1.6 - - - +
209A HIS* 3.7 29.4 + - + +
212A ALA* 4.4 8.7 - - - +
216A GLN* 5.7 3.2 - - - +
360C LYS* 4.9 19.7 - - - +
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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