Contacts of the strand formed by residues 67 - 71 (chain A) in PDB entry 1RI4
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 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLY 3.9 1.5 + - - -
66A ASP* 1.3 72.9 - - - +
68A VAL* 1.3 61.9 + - - +
89A GLU* 3.3 40.3 + - - +
132A LYS* 6.0 0.2 - - - +
133A GLU 4.8 4.1 + - - -
134A PHE* 3.6 17.4 - - - +
135A ASP* 3.1 37.3 + - - +
136A VAL 3.2 8.7 + - - +
165A ARG* 5.7 4.3 - - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 4.8 3.8 - - + -
66A ASP* 4.7 3.1 - - + +
67A SER* 1.3 79.1 + - - +
69A LEU* 1.3 65.9 + - - +
70A ASP* 4.3 3.1 - - - +
82A TYR* 3.6 50.3 - - + +
87A ILE* 4.0 20.2 - - + -
89A GLU 2.9 11.3 + - - +
90A TYR* 3.6 6.0 - - + -
91A TYR 2.8 31.9 + - - -
134A PHE* 3.5 9.5 - - - -
136A VAL* 3.2 22.7 - - + +
138A SER* 4.8 3.4 - - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 1.3 72.7 - - - +
70A ASP* 1.3 59.2 + - - +
71A LEU* 3.4 28.0 + - + -
91A TYR* 3.4 25.6 - - + +
93A VAL* 4.3 6.5 - - + -
128A MET* 4.3 4.7 - - + -
130A LEU* 3.5 28.9 - - + -
134A PHE* 3.6 32.5 - - + -
136A VAL 3.0 8.1 + - - -
137A ILE* 3.4 19.3 - - + +
138A SER 2.9 27.5 + - - +
159A ASN 5.7 0.2 - - - +
160A ILE* 6.4 0.2 - - - -
163A HIS* 4.0 16.4 - - + -
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.0 2.3 - - + -
69A LEU* 1.3 70.2 - - - +
71A LEU* 1.3 65.1 + - - +
73A CYS* 3.5 22.0 + - + +
76A GLY* 5.4 0.2 - - - -
78A ASP* 4.2 18.1 + - - +
82A TYR* 4.3 7.6 + - - -
90A TYR* 2.6 45.6 + - + +
91A TYR 2.7 10.0 + - - +
93A VAL 3.1 25.1 + - - +
138A SER* 3.5 24.0 + - - +
139A SER* 5.0 0.7 - - - -
140A GLN* 5.0 3.6 + - - +
299A SAM 5.3 2.3 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.8 23.8 - - + -
70A ASP* 1.3 68.9 - - - +
72A GLY* 1.3 64.5 + - - +
73A CYS 3.5 0.2 + - - -
93A VAL* 3.9 6.7 - - + -
123A SER* 3.9 14.6 - - - +
124A TYR* 3.7 30.7 - - + +
128A MET* 3.9 23.3 - - + -
137A ILE* 4.0 19.3 - - + -
138A SER 2.9 10.7 + - - +
139A SER* 3.5 14.9 + - - +
140A GLN 4.4 1.7 + - - -
142A SER* 3.4 11.4 + - - -
159A ASN* 6.2 0.9 - - + -
160A ILE* 3.9 31.2 - - + -
170A PHE* 4.9 4.0 - - + -
299A SAM 5.2 0.2 + - - -
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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