Contacts of the strand formed by residues 139 - 145 (chain C) in PDB entry 4XCS
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 LEU 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ALA* 3.6 31.6 - - + -
7C LYS 3.7 27.6 - - - +
8C ILE* 3.6 9.8 - - + +
9C GLY 2.9 29.5 + - - -
10C HIS 3.0 11.1 + - - +
12C ALA* 3.9 12.4 - - + +
13C PRO* 5.2 2.2 - - + -
116C TYR* 4.9 2.2 - - + -
131C PHE* 3.9 20.2 - - + -
132C ILE 3.7 14.8 - - - +
133C ILE* 4.1 11.4 - - + +
137C GLY 3.8 2.0 + - - -
138C ILE* 1.3 74.4 - - - +
140C ARG* 1.3 58.8 + - - +
141C GLN 3.7 13.2 - - - +
142C ILE* 3.9 15.3 - - + -
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Residues in contact with ARG 140 (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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8C ILE* 3.6 5.9 - - - +
38C TYR* 3.3 14.3 + - + +
132C ILE* 2.8 13.0 + - + +
133C ILE 4.6 0.4 - - - -
134C ASP* 3.2 39.5 + - + +
138C ILE* 3.5 22.4 - - - +
139C LEU* 1.3 78.4 - - - +
141C GLN* 1.3 60.8 + - - +
163C PHE* 3.4 32.5 - - + -
166C THR* 5.2 3.2 + - - -
167C ASP* 2.8 27.7 + - - -
145D ASN* 3.1 25.5 - - - +
146D ASP* 2.8 51.3 + - - +
147D LEU* 5.0 0.6 - - - +
148D PRO* 5.2 1.8 - - - +
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Residues in contact with GLN 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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8C ILE* 3.6 1.9 - - - +
130C LEU* 4.4 4.7 - - + +
131C PHE* 3.3 6.4 - - - -
132C ILE* 3.1 34.6 + - + -
139C LEU* 3.7 7.3 - - - +
140C ARG* 1.3 82.1 - - - +
142C ILE* 1.3 74.2 - - - +
143C THR* 2.8 27.4 - - + +
151C ARG* 5.2 0.8 - - - +
159C LEU* 3.5 38.3 - - - +
163C PHE* 3.7 8.3 - - + -
143D THR* 3.6 13.6 - - + +
144D VAL 3.2 13.2 - - - +
145D ASN* 3.1 20.1 + - + -
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Residues in contact with ILE 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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1C MET* 3.7 48.9 - - + -
6C ALA* 4.2 9.4 - - + +
8C ILE* 3.9 11.9 - - + -
116C TYR 5.6 1.3 - - - +
130C LEU 3.6 3.4 - - - -
131C PHE* 3.8 30.1 - - + -
139C LEU* 3.9 22.0 - - + -
141C GLN* 1.3 77.9 - - - +
143C THR* 1.3 69.1 + - - +
144C VAL* 4.2 15.9 - - + +
142D ILE* 3.7 1.6 - - + +
143D THR* 3.2 4.3 - - - -
144D VAL* 2.8 41.2 + - + +
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Residues in contact with THR 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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128C ARG 3.9 0.2 - - - +
129C GLY* 3.2 3.3 - - - -
130C LEU* 2.8 46.2 + - + +
141C GLN* 2.8 33.9 - - + +
142C ILE* 1.3 72.6 - - - +
144C VAL* 1.3 65.4 + - - +
151C ARG* 3.8 12.3 + - - +
201C GOL 3.6 22.5 + - - -
141D GLN* 4.3 8.6 + - - +
142D ILE 3.3 2.4 + - - -
143D THR* 3.0 26.0 + - - +
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Residues in contact with VAL 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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1C MET* 5.2 4.3 - - + -
117C GLY 5.5 0.9 - - - +
118C VAL* 3.7 29.8 - - + -
127C PHE* 3.9 12.6 - - + -
128C ARG 3.4 5.6 - - - +
129C GLY* 3.9 7.9 - - - -
131C PHE* 4.9 0.4 - - + -
142C ILE* 4.2 17.0 - - + -
143C THR* 1.3 78.4 - - - +
145C ASN* 1.3 64.7 + - - +
8D ILE* 3.6 17.1 - - + +
141D GLN* 3.3 2.3 - - - +
142D ILE* 2.9 57.5 + - + +
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Residues in contact with ASN 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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126C SER 3.7 0.5 - - - +
127C PHE* 3.2 3.8 - - - -
128C ARG* 3.1 29.6 + - - +
143C THR* 4.8 0.2 + - - -
144C VAL* 1.3 76.8 - - - +
146C ASP* 1.3 62.1 + - - +
147C LEU* 3.0 24.8 + - - +
201C GOL 2.9 42.7 + - - -
8D ILE* 4.3 8.0 - - - +
140D ARG 3.1 18.4 - - - +
141D GLN* 3.0 30.8 + - + -
159D LEU* 5.0 0.6 - - - +
163D PHE* 4.0 2.0 - - + -
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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