Contacts of the strand formed by residues 156 - 166 (chain J) in PDB entry 3FFC
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 LYS 156 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174I MET* 3.9 14.1 - - + -
177I MET* 6.4 0.2 - - - +
179I PHE* 3.6 45.6 - - - +
150J GLU* 3.0 32.8 + - - +
151J ILE* 4.4 3.3 + - - +
154J THR* 3.5 25.4 + - - +
155J GLN* 1.3 79.9 + - - +
157J ALA* 1.3 60.1 + - - +
211J ARG* 3.8 31.6 - - + +
212J VAL 3.2 15.0 - - - +
213J SER* 4.1 4.5 - - - -
214J ALA* 3.6 8.2 - - - +
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Residues in contact with ALA 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J PRO* 3.4 25.4 - - + -
150J GLU* 3.4 4.5 - - - -
151J ILE* 3.7 13.5 - - + -
156J LYS* 1.3 70.8 - - - +
158J THR* 1.3 60.2 + - - +
159J LEU 3.9 0.6 + - - -
210J LEU 3.5 2.3 - - - +
211J ARG* 3.2 2.4 - - - -
212J VAL* 2.8 43.3 + - + +
213J SER 4.3 1.5 - - - +
214J ALA* 5.0 1.6 - - - -
217J TRP* 3.6 26.5 - - + -
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Residues in contact with THR 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I LEU* 3.3 21.5 - - - +
146I LEU* 3.7 22.8 - - + +
148I THR* 5.2 1.2 + - - -
172I LEU* 4.7 4.5 - - + +
183I SER* 6.0 0.2 - - - -
146J PRO* 3.6 11.8 - - - +
150J GLU* 2.8 31.2 + - - +
157J ALA* 1.3 70.1 - - - +
159J LEU* 1.3 72.2 + - - +
160J VAL* 4.3 0.9 - - + -
209J ARG* 3.8 24.9 - - + -
210J LEU 3.5 6.7 - - - +
211J ARG* 3.1 25.4 + - + +
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Residues in contact with LEU 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J VAL* 4.2 14.8 - - + -
144J PHE 3.5 8.3 - - - +
145J GLU* 5.6 0.2 - - - -
146J PRO* 4.2 15.5 - - + -
157J ALA 4.3 1.6 - - - +
158J THR* 1.3 76.7 - - - +
160J VAL* 1.3 59.6 + - - +
175J TRP* 3.6 23.1 - - + -
208J SER 3.8 0.3 - - - +
209J ARG* 3.2 6.1 - - - -
210J LEU* 2.8 46.1 + - + +
212J VAL* 4.1 22.7 - - + -
217J TRP* 4.2 17.9 - - + -
224J PHE* 3.5 41.1 - - + -
255J ALA* 4.9 0.7 - - + -
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Residues in contact with VAL 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I LEU* 3.6 24.2 - - + +
144I VAL* 3.9 22.4 - - + -
146I LEU* 4.2 9.2 - - + -
185I VAL* 4.0 25.1 - - + -
143J VAL* 3.6 1.0 - - - -
144J PHE* 2.7 48.1 + - + -
158J THR* 4.3 1.6 - - + -
159J LEU* 1.3 75.2 - - - +
161J CYS* 1.3 70.8 + - - +
162J LEU* 4.8 3.1 - - + -
175J TRP* 4.3 3.1 - - - -
207J SER* 4.8 4.5 - - - -
208J SER 3.3 5.8 - - - +
209J ARG* 3.7 19.5 - - + -
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Residues in contact with CYS 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J VAL* 4.6 12.6 - - - -
142J ALA 3.6 9.0 - - - -
143J VAL* 4.6 0.7 - - - +
160J VAL* 1.3 74.2 - - - +
162J LEU* 1.3 65.1 + - - +
163J ALA 4.0 0.2 - - - -
173J LEU* 4.2 8.7 - - - +
175J TRP* 3.3 17.0 - - + -
206J LEU 3.7 0.7 - - - +
207J SER* 3.1 8.0 - - - -
208J SER* 2.6 42.7 + - - +
226J CYS* 2.0 50.3 - - + -
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I SER* 6.1 0.2 - - - +
142I LYS* 4.0 15.0 - - + -
144I VAL* 3.9 19.3 - - + -
187I TRP* 3.6 64.6 - - + +
140J GLU 3.5 2.6 - - - +
141J VAL* 3.3 4.6 - - - -
142J ALA* 2.9 30.5 + - + +
144J PHE* 3.7 20.4 - - + -
160J VAL* 4.2 4.2 + - + -
161J CYS* 1.3 74.2 - - - +
163J ALA* 1.3 59.8 + - - +
164J THR* 3.8 14.7 + - + +
206J LEU 3.7 2.0 - - - +
207J SER* 3.8 17.0 - - - -
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Residues in contact with ALA 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J PRO* 4.5 2.5 - - + -
140J GLU 3.5 4.9 - - - -
141J VAL* 4.2 4.9 - - + -
161J CYS 4.0 1.2 - - - -
162J LEU* 1.3 71.3 - - - +
164J THR* 1.3 59.5 + - - +
166J PHE* 3.4 18.1 - - + -
173J LEU* 4.1 9.6 - - + +
205J ALA* 3.3 2.9 - - - -
206J LEU* 2.8 45.3 + - + +
228J VAL* 3.7 31.2 - - + -
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Residues in contact with THR 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I LYS* 3.3 29.5 + - - +
187I TRP* 4.9 2.9 - - - +
139J PRO* 3.4 1.2 - - - +
140J GLU* 2.7 56.2 + - - +
162J LEU* 3.8 28.7 + - + +
163J ALA* 1.3 80.1 - - - +
165J GLY* 1.3 64.7 + - - +
166J PHE* 3.3 4.7 + - - -
195J GLU* 3.4 13.0 - - - +
204J TYR 3.5 3.6 - - - -
205J ALA* 4.4 7.6 - - + +
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Residues in contact with GLY 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J PHE* 3.2 8.0 - - - +
138J PRO 3.3 5.1 - - - +
140J GLU* 5.6 1.8 - - - -
164J THR* 1.3 72.3 - - - +
166J PHE* 1.3 59.9 + - - +
195J GLU* 3.1 26.6 + - - -
203J ARG* 2.7 43.5 + - - -
204J TYR 2.9 8.8 + - - -
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Residues in contact with PHE 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J PHE 3.3 12.8 - - - +
138J PRO 3.8 0.4 - - - -
139J PRO* 3.6 32.5 - - + -
163J ALA* 3.4 25.6 - - + -
164J THR 4.0 2.0 - - - -
165J GLY* 1.3 79.1 - - - +
167J TYR* 1.3 61.0 + - - +
168J PRO 3.6 14.8 - - - -
169J ASP* 3.9 12.3 - - - -
171J VAL* 3.6 35.4 - - + -
192J PRO* 4.4 4.0 - - + -
203J ARG* 3.6 0.6 - - - -
204J TYR* 2.7 73.0 + + + +
205J ALA* 4.0 1.8 - - - -
206J LEU* 3.9 17.7 - - + -
230J PHE* 4.4 1.3 - - + -
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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