Contacts of the strand formed by residues 178 - 186 (chain C) in PDB entry 3S8W
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 ASN 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C GLN 4.9 0.2 - - - -
147C SER* 2.9 26.5 - - - -
148C GLU 4.8 0.9 + - - -
177C THR* 1.3 75.6 - - - +
179C TYR* 1.3 62.1 + - - +
180C CYS* 5.8 3.1 - - - -
200C CYS* 6.0 1.8 - - + +
201C THR 3.6 3.6 + - - +
202C LEU* 3.4 33.7 + - - +
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ILE* 5.0 0.4 - - - +
121C ILE* 3.8 22.2 - - + -
145C GLU* 3.6 30.7 - - + -
146C GLN 3.6 2.5 - - - -
147C SER* 3.3 23.9 + - - -
173C LEU* 3.6 25.6 - - + +
174C ILE* 3.0 39.1 + - - +
177C THR* 3.3 34.3 - - + +
178C ASN* 1.3 74.4 - - - +
180C CYS* 1.3 65.4 + - - +
181C VAL* 5.3 1.1 - - + -
199C LYS 4.1 0.2 - - - +
200C CYS* 3.2 6.1 - - - +
201C THR* 2.9 34.2 + - - +
203C LEU* 3.9 19.1 - - + -
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Residues in contact with CYS 180 (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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144C GLU 3.5 0.5 - - - +
145C GLU* 3.4 4.5 - - - +
146C GLN* 2.8 54.9 + - + +
178C ASN* 5.8 3.1 - - - -
179C TYR* 1.3 74.7 - - - +
181C VAL* 1.3 65.8 + - - +
198C LEU* 4.2 15.7 - - + -
199C LYS 3.4 3.4 - - - -
200C CYS* 2.1 45.5 - - - -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 3.7 20.7 - - + -
114C ILE* 4.1 28.5 - - + -
121C ILE* 4.7 12.6 - - + -
123C VAL* 4.7 4.0 - - + -
143C ILE* 3.9 20.0 - - + -
144C GLU 3.1 9.6 - - - +
145C GLU* 4.8 3.1 - - + -
170C ILE* 4.3 20.4 - - + -
179C TYR* 5.4 0.2 - - + -
180C CYS* 1.3 82.0 - - - +
182C SER* 1.3 67.7 + - - +
183C VAL* 4.6 2.2 - - + -
198C LEU* 3.3 7.9 - - - -
199C LYS 2.8 34.3 + - - +
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Residues in contact with SER 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 4.3 0.9 - - - -
143C ILE* 3.5 2.9 - - - -
144C GLU* 2.7 54.4 + - - +
181C VAL* 1.3 76.2 - - - +
183C VAL* 1.3 64.6 + - - +
184C TYR* 4.5 1.4 - - - -
195C LYS* 3.9 19.0 - - - +
196C SER* 3.1 24.5 + - - -
197C PRO 4.5 0.2 - - - -
198C LEU* 3.7 20.0 - - - -
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PRO* 4.1 2.6 - - - +
110C PRO* 3.9 22.4 - - + +
112C PHE* 3.4 44.0 - - + -
123C VAL* 4.7 1.1 - - + -
125C VAL* 4.3 12.1 - - + -
141C LEU* 4.3 8.3 - - + -
142C VAL 3.2 5.2 - - - +
143C ILE* 4.1 21.5 - - + -
181C VAL* 4.6 4.5 - - + -
182C SER* 1.3 80.6 + - - +
184C TYR* 1.3 70.8 + - - +
196C SER* 3.0 31.5 + - - +
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Residues in contact with TYR 184 (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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109C PRO* 5.0 1.3 - - - -
110C PRO* 4.9 4.5 - - - -
140C SER 3.6 0.2 - - - +
141C LEU* 3.6 2.6 - - - +
142C VAL* 2.7 64.7 + - + +
144C GLU* 3.5 23.3 - - + -
153C LYS* 3.0 36.7 + - - +
155C LYS* 5.3 0.2 - - - -
182C SER* 4.5 2.9 - - - -
183C VAL* 1.3 82.7 - - - +
185C LEU* 1.3 69.1 + - - +
186C GLU* 3.7 21.9 + - - -
193C VAL* 3.2 30.3 - - + -
194C ILE 3.3 22.9 - - - +
195C LYS* 3.4 24.1 - - + -
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Residues in contact with LEU 185 (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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106C SER 4.3 7.5 + - - -
107C PHE* 4.3 29.5 + - + +
108C GLU 3.4 26.7 - - - +
109C PRO* 5.3 0.8 - - - +
110C PRO* 4.2 10.1 - - + -
127C PHE* 3.8 33.7 - - + -
139C LEU* 4.6 20.9 - - + -
140C SER 3.2 12.3 - - - +
141C LEU* 4.0 5.6 - - + -
162C MSE 3.9 12.8 - - + -
184C TYR* 1.3 81.9 - - - +
186C GLU* 1.3 60.9 + - - +
193C VAL* 3.2 19.4 - - - +
194C ILE 4.8 3.6 + - - -
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Residues in contact with GLU 186 (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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139C LEU* 3.5 8.7 - - - +
140C SER* 2.8 35.6 + - - +
142C VAL* 3.8 17.0 - - + +
155C LYS* 3.4 30.1 + - - +
184C TYR* 3.7 17.6 + - + -
185C LEU* 1.3 76.0 - - - +
187C HIS* 1.3 62.1 + - - +
188C SER* 3.6 23.1 - - - +
189C ASP* 3.8 15.1 + - - +
191C GLN* 3.8 5.6 - - - -
193C VAL* 3.6 16.0 - - + +
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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