Contacts of the helix formed by residues 180 - 200 (chain A) in PDB entry 4JDL
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 GLU 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASN* 5.8 2.2 - - - -
177A THR* 3.1 37.2 + - - +
178A GLU 3.0 0.6 - - - -
179A GLU* 1.3 104.5 + - - +
181A THR* 1.3 60.2 + - - +
182A LEU 3.2 1.1 - - - -
183A SER* 3.5 9.2 - - - +
184A PHE* 2.5 40.0 + - + +
113C SER* 4.9 15.4 - - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A CYS* 4.7 1.8 - - - -
145A LEU* 5.0 8.1 - - + +
168A TYR* 4.0 5.8 + - - +
170A VAL* 4.2 23.7 - - + +
172A VAL 3.8 18.6 - - - +
174A PRO* 3.0 36.5 - - + +
176A ASN* 5.1 2.3 - - - +
177A THR 3.7 10.9 + - - -
178A GLU* 3.8 6.1 + - - +
180A GLU* 1.3 82.0 - - - +
182A LEU* 1.3 67.7 + - + +
184A PHE* 4.1 4.4 - - - +
185A VAL* 3.5 20.4 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A CYS* 3.2 32.1 - - + -
59A CYS 5.2 7.4 - - - +
60A SER* 5.4 6.5 - - - +
168A TYR* 3.4 18.4 - - + +
172A VAL 6.0 0.2 - - - +
178A GLU* 2.9 32.7 + - + +
179A GLU* 5.1 2.7 - - - -
180A GLU 3.2 0.9 - - - +
181A THR* 1.3 83.2 - - + +
183A SER* 1.3 53.9 + - - +
186A ASP* 2.7 47.7 + - - +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU 3.7 15.6 + - - -
180A GLU* 3.1 15.0 + - - +
182A LEU* 1.3 77.2 - - - +
184A PHE* 1.3 66.0 + - - +
186A ASP* 4.2 4.3 - - - -
187A THR* 2.5 32.2 + - - -
303A GOL 5.1 11.0 - - - -
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.5 35.4 - - + -
180A GLU 2.5 24.5 + - - +
181A THR* 4.1 4.9 - - - +
183A SER* 1.3 75.2 + - - +
185A VAL* 1.3 63.6 + - + +
187A THR* 3.8 3.2 - - - -
188A ILE* 3.4 43.5 + - + +
112C VAL* 3.1 29.2 - - + +
113C SER* 4.0 7.0 - - - -
114C GLY* 3.3 35.9 - - - -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.8 29.2 - - + -
148A TYR* 3.3 33.9 - - + +
168A TYR* 3.4 22.2 - - + -
181A THR 3.5 11.5 + - - +
182A LEU 3.4 1.8 + - - -
184A PHE* 1.3 82.5 - - + +
186A ASP* 1.3 55.7 + - - +
187A THR 2.6 6.3 + - - -
188A ILE* 2.4 42.4 + - + -
189A VAL* 2.7 20.7 + - + +
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 3.4 25.6 - - - +
61A SER 4.4 8.5 - - - +
168A TYR* 3.2 30.9 - - - -
182A LEU* 2.7 38.5 + - - +
183A SER* 4.6 3.4 - - - -
185A VAL* 1.3 70.8 - - - +
187A THR* 1.3 55.3 + - - +
189A VAL* 3.4 13.3 - - - +
190A ARG* 2.8 26.4 + - - +
303A GOL 5.6 4.9 - - - +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 2.5 26.1 + - - -
184A PHE 3.8 4.3 - - - -
185A VAL 2.6 3.8 + - - -
186A ASP* 1.3 73.0 - - - +
188A ILE* 1.3 60.1 + - + +
190A ARG* 2.9 26.8 + - + +
191A CYS* 2.8 41.0 + - - -
303A GOL 4.4 11.5 + - - -
112C VAL* 6.3 3.4 - - + -
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Residues in contact with ILE 188 (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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88A ASN* 6.1 0.2 - - - +
89A PHE* 5.5 14.4 - - + -
148A TYR* 6.1 0.2 - - - +
184A PHE* 3.7 44.4 - - + +
185A VAL* 2.4 33.4 + - + +
187A THR* 1.3 70.1 - - + +
189A VAL* 1.3 66.6 + - + +
191A CYS* 3.0 18.9 + - - +
192A ASN* 3.2 12.7 + - + +
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Residues in contact with VAL 189 (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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61A SER 5.2 2.9 - - - +
62A VAL* 4.5 14.1 - - + -
148A TYR* 4.2 8.5 - - - +
166A GLU* 3.7 33.7 - - + +
168A TYR* 4.4 11.7 - - + -
185A VAL* 2.7 36.8 + - + +
186A ASP* 3.4 15.0 - - - +
188A ILE* 1.3 74.6 - - + +
190A ARG* 1.3 67.1 + - - +
192A ASN* 3.1 13.8 + - - +
193A LEU* 3.3 25.6 + - + +
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASP 2.8 19.8 + - - +
187A THR* 2.9 31.3 + - - +
189A VAL* 1.3 75.8 - - - +
191A CYS* 1.3 64.9 + - - +
193A LEU* 3.6 2.7 + - - +
194A GLN* 3.1 29.4 + - + +
303A GOL 3.5 37.8 + - - -
85C VAL* 5.5 8.9 - - - +
195C SER* 5.8 0.9 - - - -
198C ARG* 3.5 42.3 - - - +
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Residues in contact with CYS 191 (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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88A ASN* 3.2 14.4 - - + +
89A PHE* 4.5 12.8 - - + -
187A THR* 2.8 27.5 + - - -
188A ILE* 3.0 8.9 + - - +
190A ARG* 1.3 79.1 - - - +
192A ASN* 1.3 52.4 + - - +
194A GLN* 3.3 12.9 + - - +
195A SER* 2.7 36.4 + - - -
191C CYS* 3.3 36.3 - - + -
194C GLN* 4.7 1.2 - - - +
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Residues in contact with ASN 192 (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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86A TYR* 3.7 17.3 - - + -
87A LYS* 4.5 11.2 - - + -
88A ASN* 3.3 14.6 - - - +
188A ILE* 3.2 8.1 + - + +
189A VAL* 3.1 10.0 + - - +
191A CYS* 1.3 75.0 - - - +
193A LEU* 1.3 60.0 + - + +
194A GLN 3.0 0.9 - - - -
195A SER* 2.6 8.1 + - - -
196A LEU* 2.4 33.8 + - - -
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Residues in contact with LEU 193 (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 VAL* 5.2 7.2 - - + -
64A GLN* 3.0 26.7 + - + +
77A VAL* 5.5 0.7 - - + -
86A TYR* 5.6 5.4 - - + +
152A THR* 4.2 14.1 - - + -
164A VAL* 5.1 9.2 - - + -
165A VAL* 5.4 0.4 - - - -
166A GLU* 3.9 33.4 - - + +
189A VAL* 3.3 34.0 + - + +
190A ARG* 4.3 2.9 - - - +
192A ASN* 1.3 80.3 - - + +
194A GLN* 1.3 57.8 + - - +
196A LEU* 3.1 29.7 + - + +
197A ALA 2.9 24.1 + - - -
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Residues in contact with GLN 194 (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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64A GLN* 3.5 12.0 - - - +
190A ARG* 3.1 22.7 + - + +
191A CYS* 3.3 9.6 + - - +
193A LEU* 1.3 79.0 - - - +
195A SER* 1.3 55.7 + - - +
197A ALA* 3.5 5.1 + - + +
198A ARG* 3.2 25.6 + - - +
191C CYS* 4.5 7.3 + - - +
194C GLN* 3.1 54.5 + - + +
195C SER* 3.5 14.1 + - - +
198C ARG* 3.6 26.5 + - - +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.0 30.2 - - - +
88A ASN* 2.7 19.8 + - - -
191A CYS* 2.7 10.9 + - - +
192A ASN 2.6 12.3 + - - -
194A GLN* 1.3 69.7 - - - +
196A LEU* 1.3 60.6 + - - +
198A ARG* 2.6 51.4 + - - +
199A SER* 3.6 9.5 + - - -
191C CYS* 5.9 0.2 - - - -
194C GLN* 3.9 6.6 + - - -
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Residues in contact with LEU 196 (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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64A GLN* 5.8 0.4 - - + -
66A ILE* 3.9 12.6 - - + -
73A VAL* 4.2 22.7 - - + +
76A LEU* 3.8 23.0 - - + +
77A VAL* 3.7 34.8 - - + -
86A TYR* 3.7 18.3 - - + -
154A LEU* 4.9 3.1 - - + -
164A VAL* 4.9 8.7 - - + -
192A ASN 2.4 19.3 + - - +
193A LEU* 3.1 35.0 - - + +
195A SER* 1.3 70.6 - - - +
197A ALA* 1.3 68.3 + - - +
199A SER* 3.2 9.9 + - - -
200A THR* 3.5 13.9 + - + +
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Residues in contact with ALA 197 (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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64A GLN* 3.6 25.6 - - - +
65A MET 5.6 0.2 - - - +
66A ILE* 3.4 21.8 - - + -
193A LEU 2.9 12.5 + - - +
194A GLN* 3.5 10.3 - - + +
195A SER 3.3 0.2 - - - -
196A LEU* 1.3 75.0 - - - +
198A ARG* 1.3 54.9 + - - +
200A THR* 2.6 32.4 + - - +
202A ARG* 4.1 8.4 - - + +
203A GLN 4.9 1.0 + - - -
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Residues in contact with ARG 198 (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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86A TYR* 3.5 9.9 + - - +
87A LYS 5.6 0.2 - - - -
88A ASN* 2.9 15.6 + - - +
194A GLN 3.2 6.4 + - - +
195A SER* 2.6 60.7 + - - +
197A ALA* 1.3 77.4 - - - +
199A SER* 1.3 78.0 + - - +
200A THR 2.9 16.7 + - - +
201A ASN* 4.9 0.7 + - - -
203A GLN 4.9 14.3 - - - +
78B ARG* 3.9 7.3 + - - -
79B ARG* 3.8 17.4 - - - +
81B ASP* 5.6 1.8 - - - +
190C ARG* 4.9 13.7 - - - +
194C GLN* 3.2 30.0 + - + +
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Residues in contact with SER 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.5 15.7 - - - +
85A VAL 4.3 1.7 + - - -
86A TYR* 4.5 3.0 - - - +
195A SER 3.6 8.7 + - - -
196A LEU 3.2 5.2 + - - -
197A ALA 3.1 0.2 + - - -
198A ARG* 1.3 91.6 + - - +
200A THR* 1.3 57.0 + - - +
75B ALA 5.5 2.4 - - - +
78B ARG* 3.0 24.8 + - - +
79B ARG* 3.3 47.6 + - - +
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 4.0 25.6 - - + -
68A ALA* 3.2 21.9 - - + +
72A SER* 4.5 15.8 + - - -
73A VAL* 4.8 6.5 - - - -
76A LEU* 5.2 6.3 - - + -
196A LEU* 3.5 18.2 - - + +
197A ALA 2.6 32.1 - - - +
198A ARG 2.9 7.5 - - - +
199A SER* 1.3 78.5 - - - +
201A ASN* 1.3 55.2 + - - +
202A ARG 2.7 13.2 + - - -
203A GLN 4.1 1.9 + - - -
78B ARG* 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