Contacts of the strand formed by residues 136 - 145 (chain C) in PDB entry 4ZXB
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 VAL 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C SER* 1.3 80.1 - - - +
137C THR* 1.3 63.7 + - - +
138C LEU* 4.1 13.9 + - + +
181C VAL 3.7 1.4 - - - +
182C THR* 3.3 4.5 - - - -
183C VAL* 3.0 55.8 + - + +
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Residues in contact with THR 137 (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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125C ALA 4.9 1.9 - - - +
136C VAL* 1.3 74.0 - - - +
138C LEU* 1.3 76.0 + - - +
180C SER* 4.0 15.5 - - - -
181C VAL 3.4 7.9 - - - +
182C THR* 3.1 23.5 + - - +
114D THR* 4.8 9.7 - - - +
116D SER* 3.5 26.1 + - - +
118D PHE* 3.3 26.5 - - + -
135D PHE* 4.7 2.2 - - + -
137D ASN* 4.5 6.7 + - - +
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Residues in contact with LEU 138 (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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124C LEU 3.6 6.3 - - - +
125C ALA* 3.8 25.8 - - + +
136C VAL* 4.9 15.7 - - + +
137C THR* 1.3 81.1 - - - +
139C GLY* 1.3 58.2 + - - +
154C TRP* 4.9 8.1 - - + -
180C SER* 3.2 8.0 - - - -
181C VAL* 2.9 48.8 + - + +
183C VAL* 4.9 15.0 - - + -
118D PHE* 4.2 4.0 - - - -
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Residues in contact with GLY 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C PRO* 3.8 1.9 - - - +
124C LEU* 2.8 44.0 + - - +
138C LEU* 1.3 76.2 - - - +
140C CYS* 1.3 61.6 + - - +
154C TRP* 3.7 9.1 - - - -
179C SER 3.2 10.8 - - - -
118D PHE* 4.4 2.3 - - - -
135D PHE* 4.1 11.0 - - - -
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Residues in contact with CYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL* 3.7 22.9 - - - -
122C TYR 3.5 8.1 - - - -
123C PRO* 5.2 1.1 - - - -
124C LEU* 3.9 4.5 - - - +
139C GLY* 1.3 76.3 - - - +
141C LEU* 1.3 59.1 + - - +
142C VAL* 4.0 3.0 + - - +
152C LEU* 4.3 6.9 - - + +
154C TRP* 3.6 14.4 - - + -
178C SER* 3.3 5.4 - - - -
179C SER* 2.9 30.7 + - - +
195C CYS* 2.0 49.1 - - + -
197C VAL* 4.3 2.5 - - - -
208C LYS* 5.5 0.2 - - - -
135D PHE* 5.0 0.2 - - - -
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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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120C SER 3.4 1.7 - - - +
121C VAL* 3.3 4.7 - - - +
122C TYR* 2.7 66.7 + - + +
124C LEU* 3.8 22.6 - - + +
140C CYS* 1.3 72.6 - - - +
142C VAL* 1.3 64.6 + - - +
143C LYS* 3.9 9.0 - - + -
176C THR* 3.8 26.9 - - + -
177C LEU 3.9 4.5 - - - +
178C SER* 4.5 9.6 - - - +
124D GLN* 4.4 3.4 - - - +
131D SER* 4.1 29.6 - - - +
133D VAL* 5.4 5.4 - - + -
178D THR* 4.8 12.1 - - + +
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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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119C PRO* 3.5 27.1 - - + -
120C SER 3.5 3.4 - - - -
121C VAL* 4.3 5.6 - - + -
140C CYS* 4.4 1.6 - - - +
141C LEU* 1.3 77.2 - - - +
143C LYS* 1.3 59.1 + - - +
145C TYR* 3.9 15.2 - - + -
150C VAL* 4.4 6.5 - - + -
152C LEU* 3.9 18.6 - - + -
176C THR* 3.4 2.8 - - - +
177C LEU* 2.8 48.8 + - + +
197C VAL* 3.8 39.7 - - + -
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Residues in contact with LYS 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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119C PRO* 3.5 1.7 - - - +
120C SER* 3.0 40.8 + - - +
122C TYR* 4.4 8.1 - - + +
141C LEU* 3.9 13.2 - - + -
142C VAL* 1.3 75.9 - - - +
144C GLY* 1.3 67.6 + - - +
145C TYR* 3.7 2.7 - - - -
171C GLN* 3.1 34.0 + - - +
175C TYR 3.7 0.2 - - - -
176C THR* 3.5 22.1 + - + +
124D GLN* 3.7 21.8 - - - +
131D SER* 3.3 26.2 + - - +
160D LEU* 6.1 0.2 - - - +
178D THR* 4.8 6.7 - - - +
179D LEU 5.6 3.0 - - - -
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Residues in contact with GLY 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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117C THR* 3.3 21.8 - - - +
118C ALA 3.6 5.6 - - - +
120C SER* 5.5 0.9 + - - -
143C LYS* 1.3 81.4 - - - +
145C TYR* 1.3 57.1 + - - -
171C GLN* 5.7 1.1 - - - -
174C LEU* 3.3 22.5 - - - +
175C TYR 3.0 13.1 + - - -
176C THR* 3.8 1.4 + - - -
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Residues in contact with TYR 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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117C THR* 3.2 15.0 - - - +
119C PRO* 3.6 34.3 - - + -
142C VAL* 3.9 20.4 - - + -
144C GLY* 1.3 76.8 - - - +
146C PHE* 1.3 67.0 + - - +
147C PRO 3.7 17.0 - - - -
148C GLU* 2.9 27.4 + - - -
150C VAL* 3.3 29.1 - - + +
168C ALA* 3.2 16.8 - - - +
174C LEU* 3.5 3.4 - - - -
175C TYR* 2.7 62.8 + + + +
176C THR 4.2 0.7 - - - -
177C LEU* 3.6 13.0 - - + +
199C HIS* 3.8 3.8 - - - +
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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