Contacts of the strand formed by residues 180 - 188 (chain I) 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 180 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15I GLU* 3.3 38.3 + - - +
16I LYS* 5.5 4.0 - - - +
92I LEU* 3.6 17.7 - - + -
122I PRO* 4.1 17.0 - - + -
123I ASN 5.7 0.2 - - - +
124I ILE* 3.3 28.0 - - + +
171I VAL* 4.8 1.3 - - + -
172I LEU 3.4 11.4 - - - +
173I ASP* 3.5 32.3 + - - +
174I MET* 5.9 0.2 - - - -
175I ARG* 5.8 0.6 - - - +
178I ASP* 3.7 13.2 + - - +
179I PHE* 1.3 88.7 - - - +
181I SER* 1.3 61.1 + - - +
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Residues in contact with SER 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I ILE* 5.0 1.6 - - - -
148I THR* 3.7 4.7 + - - -
149I ASP* 4.0 4.9 + - - -
171I VAL* 3.6 2.8 - - - +
172I LEU* 2.7 54.2 + - - +
174I MET* 6.0 0.4 - - - -
179I PHE* 3.6 8.9 - - - -
180I LYS* 1.3 75.4 - - - +
182I ASN* 1.3 71.7 + - - +
183I SER* 3.5 8.0 + - - -
211J ARG* 3.4 30.9 + - - -
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Residues in contact with ASN 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I PRO* 4.1 7.9 - - - +
124I ILE* 4.4 9.6 - - - +
148I THR* 3.2 5.0 + - - -
149I ASP* 3.0 26.5 + - - +
150I PHE* 3.5 46.9 + - + +
151I ASP* 3.7 3.6 + - - +
152I SER* 3.6 32.9 + - - +
169I LYS* 5.0 10.8 - - + +
170I CYS 3.6 4.0 - - - +
171I VAL* 3.4 25.6 - - - +
180I LYS 4.4 0.6 - - - -
181I SER* 1.3 69.7 + - - +
183I SER* 1.3 63.3 + - - +
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Residues in contact with SER 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU* 4.3 5.2 - - - -
147I PHE 3.7 6.5 - - - -
148I THR* 4.2 7.6 - - - -
150I PHE* 3.8 2.9 - - - -
169I LYS* 3.3 5.0 - - - -
170I CYS* 2.9 37.2 + - - +
172I LEU* 3.2 28.7 - - - +
181I SER* 3.5 1.0 + - - -
182I ASN* 1.3 80.1 + - - +
184I ALA* 1.3 61.4 + - - +
158J THR* 6.0 0.2 - - - -
209J ARG* 3.3 30.2 + - - -
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Residues in contact with ALA 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU* 3.5 6.4 - - - +
147I PHE* 2.8 47.7 + - + +
150I PHE* 4.3 1.3 - - + -
156I VAL* 4.0 33.7 - - + -
167I THR* 3.9 7.2 - - - +
168I ASP 4.4 4.9 - - - +
183I SER* 1.3 77.5 - - - +
185I VAL* 1.3 63.7 + - - +
199I PHE* 4.7 3.1 - - + -
209J ARG* 3.4 4.9 - - - +
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Residues in contact with VAL 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I VAL* 3.6 27.4 - - + -
145I CYS 3.4 2.9 - - - +
146I LEU* 3.9 9.6 - - + -
166I ILE* 3.4 2.8 - - - +
167I THR* 2.8 46.1 + - + +
184I ALA* 1.3 79.2 - - - +
186I ALA* 1.3 66.1 + - - +
187I TRP* 3.9 15.5 - - + -
199I PHE* 4.4 2.5 - - - -
160J VAL* 4.0 18.6 - - + -
162J LEU* 4.8 0.2 - - + -
207J SER* 4.2 4.7 - - - +
209J ARG* 3.6 33.2 - - - +
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Residues in contact with ALA 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I VAL* 3.5 1.4 - - - -
145I CYS* 2.8 32.6 + - + +
164I VAL* 5.3 0.2 - - + -
165I TYR 3.2 11.9 - - - +
166I ILE* 3.7 15.3 - - + -
185I VAL* 1.3 76.3 - - - +
187I TRP* 1.3 66.5 + - - +
193I PHE* 4.3 15.9 - - + -
198I ALA* 4.6 2.9 - - + -
199I PHE* 3.6 25.1 - - + -
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Residues in contact with TRP 187 (chain I).
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* 3.7 32.5 - - + +
143I SER 3.4 16.6 - - - +
144I VAL* 3.8 11.9 - - + -
163I ASP 4.3 0.2 - - - +
164I VAL* 3.8 1.9 - - - +
165I TYR* 3.0 62.9 + + + +
167I THR* 3.6 26.9 - - + -
185I VAL* 3.9 7.2 - - + -
186I ALA* 1.3 84.9 - - - +
188I SER* 1.3 72.1 + - - +
189I ASN* 5.3 0.2 - - - -
193I PHE* 4.0 6.1 - - - -
162J LEU* 3.6 40.2 - - + +
164J THR* 4.9 1.4 - - + +
193J LEU* 3.7 21.3 - - + -
195J GLU* 5.8 1.0 + - - -
205J ALA* 3.8 25.8 - - + -
206J LEU 5.2 2.0 - - - -
207J SER* 4.5 3.1 - - - -
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Residues in contact with SER 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I ASP 4.2 0.7 - - - +
142I LYS* 3.5 4.9 - - - -
143I SER* 3.5 25.4 + - - +
163I ASP 2.5 26.1 + - - -
164I VAL* 3.0 17.9 - - - +
165I TYR* 5.5 1.6 - - - -
187I TRP* 1.3 84.1 + - - +
189I ASN* 1.3 68.1 + - - +
190I LYS* 4.0 8.7 - - - +
193I PHE* 3.8 27.0 - - - +
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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