Contacts of the strand formed by residues 140 - 147 (chain C) in PDB entry 3SE3
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 SER 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C ASP 3.8 4.0 + - - -
139C LEU* 1.3 74.8 + - - +
141C LEU* 1.3 61.3 + - - +
142C VAL* 5.4 1.1 - - - -
155C LYS* 2.5 33.6 + - - +
185C LEU* 3.7 5.4 - - - -
186C GLU* 2.7 59.4 + - - +
187C HIS 5.5 0.7 + - - -
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Residues in contact with LEU 141 (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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110C PRO* 5.1 5.2 - - + -
125C VAL* 5.2 7.4 - - + -
127C PHE* 4.6 18.4 - - + -
139C LEU 4.3 0.6 + - - -
140C SER* 1.3 70.7 - - - +
142C VAL* 1.3 76.5 + - - +
143C ILE* 4.5 5.6 - - + +
155C LYS* 3.4 31.0 - - - +
156C PRO* 4.0 16.1 - - + +
166C PHE* 4.2 29.4 - - + -
168C TYR* 6.3 0.2 - - + -
183C VAL* 4.7 11.2 - - + -
184C TYR 3.9 5.2 - - - +
185C LEU* 3.8 25.5 - - + +
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Residues in contact with VAL 142 (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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140C SER* 4.5 2.2 - - - +
141C LEU* 1.3 83.3 - - - +
143C ILE* 1.3 63.6 + - - +
144C GLU* 3.7 1.5 + - + +
153C LYS* 3.7 34.5 - - + -
154C HIS 3.3 4.0 - - - +
155C LYS* 5.3 6.1 - - + -
183C VAL* 3.5 3.1 - - - +
184C TYR* 3.1 73.8 + - + +
186C GLU* 3.6 28.3 - - + +
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Residues in contact with ILE 143 (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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123C VAL* 5.6 6.3 - - + -
125C VAL* 6.2 2.0 - - + -
141C LEU* 4.1 7.5 - - + +
142C VAL* 1.3 71.7 - - - +
144C GLU* 1.3 60.2 + - - +
154C HIS* 2.8 49.8 + - + +
156C PRO* 5.4 3.8 - - + -
168C TYR* 4.8 16.4 - - + -
170C ILE* 5.6 4.9 - - + -
181C VAL* 5.5 2.9 - - + -
182C SER 4.0 3.6 - - - -
183C VAL* 4.1 17.3 - - + -
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Residues in contact with GLU 144 (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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142C VAL* 3.7 4.5 + - + -
143C ILE* 1.3 72.8 - - - +
145C GLU* 1.3 61.3 - - - +
146C GLN* 3.9 10.5 - - + +
151C VAL* 4.3 22.2 - - + +
152C LYS 3.3 11.7 - - - +
153C LYS* 5.0 4.3 - - + +
154C HIS* 4.7 0.2 - - - -
170C ILE* 5.0 0.7 - - - +
181C VAL* 3.3 25.6 - - - +
182C SER* 2.8 34.7 + - - +
184C TYR* 3.8 19.0 + - + +
195C LYS* 2.9 36.6 + - - +
198C LEU* 5.5 0.2 - - - +
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Residues in contact with GLU 145 (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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121C ILE* 6.3 1.3 - - + -
143C ILE 3.7 0.4 + - - -
144C GLU* 1.3 74.6 - - - +
146C GLN* 1.3 61.0 + - - +
147C SER* 4.8 2.6 + - - +
150C ILE 3.6 1.7 - - - +
151C VAL* 3.4 1.3 - - - -
152C LYS* 2.7 71.3 + - + +
154C HIS* 2.9 33.0 + - + +
170C ILE* 3.3 32.1 - - + +
171C ASP 5.5 0.2 - - - +
173C LEU* 3.8 14.7 - - + +
179C TYR* 4.1 22.9 - - + -
180C CYS 4.3 1.1 - - - -
181C VAL* 4.7 5.4 - - + -
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Residues in contact with GLN 146 (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* 3.9 10.6 - - - +
145C GLU* 1.3 78.8 - - - +
147C SER* 1.3 61.9 + - - +
149C GLY* 5.3 5.3 - - - +
150C ILE 3.2 9.0 - - - +
151C VAL* 3.6 26.3 - - + +
179C TYR* 3.4 1.7 - - - +
180C CYS* 2.5 54.2 + - + +
181C VAL* 5.2 0.4 - - - -
182C SER 5.3 0.2 + - - -
198C LEU* 3.4 39.1 - - - +
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Residues in contact with SER 147 (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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145C GLU* 4.8 3.0 + - - +
146C GLN* 1.3 73.1 - - - +
148C GLU* 1.3 71.1 + - - +
149C GLY 3.0 2.9 - - - +
150C ILE* 2.7 42.2 + - - +
177C THR* 4.9 0.4 - - - -
178C ASN 3.6 14.4 - - - -
179C TYR* 3.1 41.4 - - - +
180C CYS* 4.6 0.4 - - - +
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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