Contacts of the helix formed by residues 151 - 170 (chain C) in PDB entry 3WF4
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 ASP 151 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS* 3.0 26.5 + - - -
144C SER 4.4 1.0 - - - +
145C ILE* 3.4 9.8 - - - -
146C LEU* 3.0 36.9 + - + +
149C SER* 2.9 17.1 + - - +
150C SER* 1.3 75.2 - - - +
152C PRO* 1.4 64.0 - - - +
153C ASP* 2.9 16.5 + - - +
154C TYR* 3.1 9.1 + - + +
155C LEU* 2.8 23.9 + - - +
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Residues in contact with PRO 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 4.9 2.0 - - - +
150C SER 3.5 9.4 - - - +
151C ASP* 1.4 82.2 - - - +
153C ASP* 1.3 68.5 + - - +
155C LEU* 3.7 9.4 - - + +
156C ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 5.6 0.4 - - - -
142C LYS* 2.7 41.8 + - + +
145C ILE* 4.6 4.7 - - + -
151C ASP* 2.9 6.8 + - - +
152C PRO* 1.3 79.7 - - - +
154C TYR* 1.3 65.7 + - - +
156C ALA* 3.1 5.2 + - - +
157C ALA* 3.1 24.7 + - - +
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Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TRP* 4.6 0.2 - + - -
124C PRO* 3.8 10.0 - - - +
125C TYR* 4.8 0.5 - - - +
135C LEU* 3.9 23.0 - - + +
139C LEU* 4.4 10.3 - - + -
145C ILE* 3.9 16.3 - - + +
146C LEU 4.0 10.3 - - - +
147C LEU* 4.1 18.8 - - + -
148C ARG* 3.2 33.5 + - - +
149C SER 3.2 19.1 - - - -
151C ASP* 3.1 14.4 + - + +
153C ASP* 1.3 76.5 - - - +
155C LEU* 1.3 64.5 + - + +
157C ALA* 3.3 5.0 + - - +
158C VAL* 2.9 43.2 + - + +
186C GLU* 4.3 0.2 + - - -
199C TYR* 2.9 41.2 + + - -
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C SER 3.4 19.7 - - - +
150C SER* 3.7 27.4 - - - +
151C ASP 2.8 21.3 + - - +
152C PRO* 3.9 8.7 - - + +
154C TYR* 1.3 76.2 - - + +
156C ALA* 1.3 58.1 + - - +
158C VAL* 3.1 5.1 + - + +
159C ASP* 2.8 32.0 + - - +
199C TYR* 3.9 15.3 - - + -
202C PHE* 3.7 50.5 - - + -
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PRO 2.9 19.0 + - - +
153C ASP* 3.1 6.9 + - - +
155C LEU* 1.3 75.3 - - - +
157C ALA* 1.3 63.3 + - - +
159C ASP* 3.6 7.4 + - - +
160C LYS* 3.1 22.9 + - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TRP* 3.8 9.5 - - + -
90C GLU* 5.4 0.3 - - - +
138C TRP* 4.2 16.0 - - + -
139C LEU* 3.7 27.8 - - + -
153C ASP 3.1 9.5 + - - +
154C TYR 3.7 7.2 - - - +
156C ALA* 1.3 75.1 - - - +
158C VAL* 1.3 65.7 + - - +
160C LYS* 3.1 8.1 + - - +
161C TRP* 3.0 23.0 + - - +
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TRP* 3.7 23.3 - - + -
124C PRO* 4.0 12.6 - - + -
154C TYR* 2.9 49.7 + - + +
155C LEU* 3.5 8.5 - - + +
157C ALA* 1.3 78.7 - - - +
159C ASP* 1.3 53.4 + - - +
161C TRP* 3.0 3.6 + - - +
162C LEU* 2.8 45.6 + - + +
199C TYR* 5.2 0.9 - - + -
202C PHE* 4.2 7.2 - - + -
203C LEU* 3.9 26.5 - - + -
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Residues in contact with ASP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LEU 2.8 19.8 + - - +
156C ALA* 3.7 8.5 - - - +
158C VAL* 1.3 76.7 - - - +
160C LYS* 1.3 56.0 + - - +
162C LEU* 3.4 6.8 + - - +
163C GLY* 2.9 24.4 + - - -
202C PHE* 3.8 17.9 - - + -
206C ARG* 2.8 47.5 + - - +
210C HIS* 5.0 1.2 + - - -
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Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 4.9 4.3 + - - +
93C PRO* 4.9 6.3 - - - +
94C GLY* 4.2 23.0 - - - +
96C TYR* 4.3 16.4 + - - +
156C ALA 3.1 12.7 + - - +
157C ALA* 3.1 11.2 + - - +
159C ASP* 1.3 75.6 - - - +
161C TRP* 1.3 63.5 + - - +
163C GLY* 3.1 11.7 + - - -
164C VAL* 3.3 17.7 + - + +
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Residues in contact with TRP 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 4.1 8.9 - - + +
86C TRP* 3.3 77.5 - + + +
89C HIS* 3.6 27.8 - + + -
90C GLU* 4.0 13.3 + - + +
96C TYR* 4.4 13.7 - + - -
98C PHE* 3.8 22.7 - + - -
122C PRO 4.5 9.3 + - - -
124C PRO* 4.7 6.3 - - + +
157C ALA 3.0 5.8 + - - +
158C VAL 3.4 6.1 - - - +
160C LYS* 1.3 73.6 - - - +
162C LEU* 1.3 77.8 + - + +
164C VAL* 3.1 8.7 + - + -
165C LEU* 3.0 59.6 + - + +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C PRO* 5.4 4.7 - - + +
124C PRO* 5.2 6.7 - - + -
158C VAL* 2.8 43.1 + - + +
159C ASP* 3.9 8.3 - - - +
161C TRP* 1.3 87.9 - - + +
163C GLY* 1.3 58.1 + - - +
165C LEU* 4.8 3.1 - - + -
166C LEU* 2.9 52.0 + - + +
167C PRO* 3.4 1.7 - - - +
202C PHE* 5.2 0.4 - - + -
203C LEU* 4.4 4.9 - - + -
206C ARG* 4.0 23.8 - - + -
207C PHE* 3.8 35.7 - - + -
210C HIS* 3.7 10.1 - - + -
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ASP 2.9 15.2 + - - -
160C LYS* 3.1 7.3 + - - -
162C LEU* 1.3 77.6 - - - +
164C VAL* 1.3 58.6 + - - +
167C PRO* 3.5 18.2 - - - +
210C HIS* 3.7 19.3 + - - -
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 3.7 41.7 - - + +
98C PHE* 3.9 29.8 - - + -
160C LYS* 3.3 10.9 + - + +
161C TRP* 3.1 9.2 + - + +
163C GLY* 1.3 80.3 - - - +
165C LEU* 1.3 62.9 + - - +
166C LEU 3.7 0.2 - - - -
167C PRO* 3.6 6.8 - - - +
168C LYS* 3.5 23.2 + - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 4.0 23.8 - - + -
98C PHE* 4.4 13.2 - - + -
104C VAL* 4.7 3.6 - - + -
122C PRO* 3.8 28.3 - - + +
161C TRP* 3.0 52.2 + - + +
162C LEU* 4.6 2.7 - - + +
164C VAL* 1.3 77.7 - - - +
166C LEU* 1.3 76.0 + - + +
168C LYS* 3.0 11.6 + - + +
169C MET* 3.0 42.4 + - + +
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 5.7 1.1 - - + -
122C PRO* 4.7 15.0 - - + -
162C LEU* 2.9 39.2 + - + +
165C LEU* 1.3 92.1 - - + +
167C PRO* 1.3 61.7 - - - +
169C MET* 2.8 13.7 + - + +
170C LYS* 2.8 25.0 + - - -
183C VAL* 5.9 0.2 - - + -
206C ARG 4.3 0.2 - - - +
207C PHE* 3.9 42.4 - - + -
210C HIS* 3.5 23.3 - - + -
211C LEU* 3.6 22.9 - - + +
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Residues in contact with PRO 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LEU 3.4 11.7 - - - +
163C GLY 3.5 21.5 - - - +
164C VAL 3.6 4.3 - - - +
165C LEU 3.5 2.9 - - - -
166C LEU* 1.3 88.7 - - + +
168C LYS* 1.3 59.0 + - + +
170C LYS* 3.8 9.3 - - + +
171C PRO* 3.0 25.5 - - - +
210C HIS* 3.9 20.6 - - + +
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C PHE* 3.6 51.5 - - + -
105C GLU* 3.4 43.8 + - + +
164C VAL* 3.5 21.4 + - - +
165C LEU* 3.0 12.0 + - + +
167C PRO* 1.3 77.6 - - + +
169C MET* 1.3 67.8 + - + +
171C PRO* 3.5 12.4 - - - +
172C LEU* 3.8 15.2 - - - +
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Residues in contact with MET 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C VAL* 5.3 0.9 - - - -
104C VAL* 4.4 12.8 - - + -
105C GLU* 4.1 15.5 - - + -
108C LEU* 3.7 26.2 - - + -
120C LEU* 3.7 30.7 - - + -
165C LEU* 3.0 35.4 + - + +
166C LEU* 2.8 15.5 + - + +
168C LYS* 1.3 94.3 - - + +
170C LYS* 1.3 65.2 + - - +
172C LEU* 2.8 24.8 + - + +
173C LEU* 3.3 14.5 + - + +
180C VAL* 5.5 1.5 - - + +
211C LEU* 4.4 9.6 - - + -
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LEU 2.8 18.6 + - - +
167C PRO* 3.8 7.2 - - + +
169C MET* 1.3 71.7 - - - +
171C PRO* 1.4 72.4 - - + +
172C LEU 3.1 0.9 + - - -
173C LEU* 3.1 12.1 + - + +
176C ASN* 3.0 32.8 + - - +
210C HIS 3.6 24.0 + - - +
211C LEU* 4.0 24.9 - - - +
212C GLY* 5.2 1.8 - - - +
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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
------------------------------------------------------------
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