Contacts of the strand formed by residues 137 - 141 (chain C) in PDB entry 3RKR
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 HIS 137 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLN* 5.7 2.2 - - - -
85C ASP 2.8 12.3 + - - +
86C VAL* 3.3 12.0 - - + +
87C LEU 2.8 30.3 + - - -
130C MET* 3.8 1.6 - - - +
136C GLY* 1.3 80.4 + - - -
138C ILE* 1.3 57.5 + - - +
139C ILE* 4.0 19.6 - - + +
180C ARG* 3.2 53.6 + - + +
182C SER* 5.9 0.6 + - - -
219C LEU* 3.2 27.9 + - - +
220C ALA* 3.4 22.4 + - - -
222C GLN* 4.6 8.8 + - + -
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Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.4 18.2 - - + +
89C ASN* 4.0 23.3 - - - +
123C LEU* 3.8 44.2 - - + +
126C PHE 5.8 0.2 - - - -
127C ALA* 4.8 6.3 - - + +
130C MET* 3.9 27.1 - - + -
137C HIS* 1.3 75.4 - - - +
139C ILE* 1.3 56.6 + - - +
140C ASN* 3.7 10.7 + - - +
167C MET* 4.7 0.4 - - - -
174C LEU* 4.3 15.0 - - + -
179C VAL* 4.6 2.7 - - + -
180C ARG 2.9 6.5 + - - +
181C VAL* 3.2 11.9 - - + -
182C SER* 2.7 33.3 + - - +
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Residues in contact with ILE 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C VAL* 3.9 24.5 - - + -
87C LEU 2.9 11.7 + - - +
88C VAL* 3.3 10.4 - - + +
89C ASN 2.8 30.8 + - - -
137C HIS* 4.1 14.6 - - + +
138C ILE* 1.3 76.0 - - - +
140C ASN* 1.3 59.3 + - - +
141C ILE* 4.3 3.8 - - + -
182C SER* 3.5 21.8 - - - +
184C VAL* 3.9 23.1 - - + -
216C VAL* 3.9 42.0 - - + +
219C LEU* 4.1 8.7 - - + -
220C ALA 4.0 11.7 - - - +
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Residues in contact with ASN 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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89C ASN* 2.9 34.8 + - + +
138C ILE* 3.7 7.3 + - - +
139C ILE* 1.3 74.2 - - - +
141C ILE* 1.3 60.3 + - - +
142C SER 3.6 0.5 + - - -
163C LEU* 4.3 11.7 - - + +
167C MET* 3.4 42.6 - - + +
181C VAL* 3.6 9.5 - - - +
182C SER 2.9 25.7 + - - +
183C LEU* 3.6 16.0 - - + +
184C VAL* 2.7 34.3 + - - +
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Residues in contact with ILE 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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18C ILE* 4.4 10.5 - - + -
22C ILE* 4.0 7.0 - - + -
88C VAL* 4.1 11.7 - - + -
89C ASN 3.0 21.1 + - - +
90C ASN* 4.0 30.6 - - - +
139C ILE* 4.3 5.6 - - + -
140C ASN* 1.3 75.4 - - - +
142C SER* 1.3 60.2 + - - +
143C SER 4.1 1.4 + - - -
160C LYS* 4.6 8.3 + - - -
163C LEU* 4.0 10.7 - - - +
184C VAL* 3.8 16.4 - - + +
204C LEU* 4.1 27.8 - - + -
212C ILE* 4.3 6.7 - - + -
216C VAL* 3.7 30.1 - - + -
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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