Contacts of the strand formed by residues 121 - 125 (chain C) in PDB entry 5Z7R
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 ILE 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B GLY* 4.0 13.9 - - - +
159B LYS* 4.3 0.2 - - + -
160B GLN* 3.4 50.3 - - + +
163B PHE* 4.0 20.0 - - + -
99C PRO* 5.5 0.9 - - + -
100C VAL 3.1 6.5 + - - +
101C ILE* 3.3 18.4 - - + +
102C ALA* 2.6 35.0 + - - +
119C CYS* 3.4 0.9 - - - +
120C ASP* 1.3 89.2 - - + +
122C ARG* 1.3 61.8 + - - +
123C ILE* 4.0 13.5 - - + -
180C ASN* 3.6 6.3 - - - +
195C ILE* 4.7 3.6 - - + -
199C ILE* 4.3 15.7 - - + -
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLY* 4.1 20.8 - - - +
102C ALA* 3.5 15.9 - - + +
104C VAL* 4.6 4.0 - - + -
116C ALA* 2.9 43.4 + - + +
117C MET* 3.3 16.1 + - - +
119C CYS 2.8 30.7 + - - -
120C ASP 4.2 3.6 + - - -
121C ILE* 1.3 74.6 - - - +
123C ILE* 1.3 65.3 + - - +
130C PHE* 5.2 3.4 - - - -
152C LEU* 3.9 26.7 - - - +
178C LEU* 2.9 40.3 + - - +
179C VAL* 3.3 10.2 - - + -
180C ASN* 2.9 32.4 + - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN* 3.5 17.7 - - - +
101C ILE* 4.8 4.9 - - + -
102C ALA 2.9 11.4 + - - +
103C ALA* 4.2 6.7 - - + -
104C VAL* 2.8 27.5 + - - +
121C ILE* 4.0 4.5 - - + -
122C ARG* 1.3 82.5 - - - +
124C ALA* 1.3 61.2 + - - +
179C VAL* 4.6 1.3 - - - -
180C ASN* 4.0 9.2 - - + -
181C LYS* 3.8 26.5 - - + +
183C VAL* 5.7 2.7 - - + -
188C LEU* 3.3 25.4 - - + +
191C THR* 4.2 14.4 - - - +
192C ALA* 4.7 7.6 - - + +
195C ILE* 3.4 31.4 - - + -
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.1 14.1 - - + +
123C ILE* 1.3 76.0 - - - +
125C SER* 1.3 65.5 + - - +
128C ALA* 4.1 9.9 - - + -
130C PHE* 4.4 4.9 - - + -
170C ALA* 4.7 2.2 - - + -
179C VAL* 4.1 17.3 - - + -
181C LYS 3.0 13.2 + - - +
182C VAL* 3.1 16.0 - - + -
183C VAL* 3.0 26.2 + - - +
188C LEU* 3.7 6.7 - - - -
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Residues in contact with SER 125 (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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104C VAL 2.7 10.4 + - - -
105C ASN* 3.1 20.1 + - - -
106C GLY 4.1 0.2 + - - -
124C ALA* 1.3 72.8 - - - +
126C SER* 1.3 54.9 + - - +
127C ASN* 2.5 30.1 + - - -
128C ALA* 2.8 32.4 + - - +
170C ALA* 3.9 2.9 - - - +
182C VAL* 4.2 0.9 - - - -
183C VAL 3.2 6.7 - - - -
184C GLU 4.7 0.2 - - - -
185C PRO* 3.7 22.4 - - - -
188C LEU* 3.7 17.4 - - - +
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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