Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 1MRJ
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 TYR 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.2 3.5 - - - -
65A ASP 2.9 25.0 + - - -
68A ASN* 2.9 19.2 + - - -
69A VAL* 1.3 78.5 - - - +
71A ILE* 1.3 63.8 + - - +
72A MET* 3.4 10.7 + - - +
163A ARG* 4.3 0.7 - - - +
300A ADN 3.4 15.3 - - - -
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Residues in contact with ILE 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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62A VAL* 3.5 29.6 - - + -
63A ALA 3.6 3.6 - - - -
64A ILE* 4.0 9.6 - - + -
70A TYR* 1.3 70.6 - - - +
72A MET* 1.3 66.0 + - - +
73A GLY* 3.8 12.1 - - - +
74A TYR* 5.8 0.4 - - + -
83A PHE* 3.4 21.0 - - + -
85A GLU* 5.4 0.7 - - - +
151A LEU* 5.5 3.8 - - + -
154A LEU* 3.8 21.5 - - + -
155A ILE* 3.7 27.6 - - + -
158A THR* 3.4 23.8 - - - +
159A SER* 3.7 11.4 - - - +
300A ADN 2.9 29.5 + - - +
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Residues in contact with MET 72 (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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47A TYR* 4.1 10.1 - - + -
63A ALA* 2.8 20.4 + - + +
65A ASP* 4.0 25.1 - - + +
68A ASN* 5.1 3.4 - - - +
70A TYR* 3.8 19.1 - - - +
71A ILE* 1.3 80.8 - - - +
73A GLY* 1.3 59.6 + - - +
82A PHE* 3.7 6.3 - - + -
83A PHE* 3.3 27.2 + - - -
85A GLU* 5.4 5.6 - - - +
87A SER* 3.7 46.7 - - - +
88A ALA* 3.7 11.7 - - + +
91A ALA* 3.8 22.2 - - + -
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Residues in contact with GLY 73 (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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62A VAL* 3.6 6.6 - - - +
63A ALA* 2.9 23.8 + - - +
71A ILE* 3.6 7.9 - - - +
72A MET* 1.3 81.1 - - - +
74A TYR* 1.3 64.6 + - - +
81A TYR 3.0 15.7 - - - -
82A PHE* 4.1 6.1 - - - -
83A PHE* 4.7 3.8 - - - -
96A PHE* 4.2 5.2 - - - -
105A LEU* 5.9 1.6 - - - -
151A LEU* 6.5 0.4 - - - -
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Residues in contact with TYR 74 (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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60A ILE* 4.2 13.0 - - + -
61A SER 3.1 13.9 - - - +
62A VAL* 4.2 15.9 - - + -
71A ILE* 5.8 0.2 - - + -
73A GLY* 1.3 77.1 - - - +
75A ARG* 1.3 69.9 + - - +
76A ALA* 4.0 5.8 - - + -
80A SER* 3.4 2.3 - - - -
81A TYR* 2.7 71.6 + + + +
96A PHE* 3.5 7.6 - - - -
105A LEU* 5.1 6.3 - - + -
139A LEU* 2.7 66.0 + - + +
142A TYR* 3.5 16.8 - + - -
151A LEU* 4.4 17.9 - - + -
154A LEU* 5.4 1.8 - - + -
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Residues in contact with ARG 75 (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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60A ILE* 3.3 8.0 - - - +
61A SER* 2.7 37.7 + - - +
74A TYR* 1.3 78.7 - - - +
76A ALA* 1.3 63.3 + - - +
77A GLY 2.5 25.8 + - - +
78A ASP* 4.0 7.1 - - - +
79A THR 3.4 13.9 - - - +
80A SER* 4.5 1.1 - - - -
96A PHE* 3.8 40.8 - - + +
98A ASP* 2.6 46.6 + - - -
99A ALA* 3.8 24.4 - - - +
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Residues in contact with ALA 76 (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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59A THR 4.6 3.8 - - - -
60A ILE* 4.2 6.1 - - + -
74A TYR* 4.0 14.3 - - + -
75A ARG* 1.3 74.7 - - - +
77A GLY* 1.3 64.5 + - - +
78A ASP* 3.1 4.3 + - - +
79A THR* 2.9 20.4 + - - +
81A TYR* 4.3 8.0 + - + +
139A LEU 4.2 0.7 - - - +
140A PHE* 3.9 40.4 - - + +
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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