Contacts of the strand formed by residues 69 - 76 (chain A) in PDB entry 3R1N
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 LYS 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 05B 5.9 0.8 - - - -
50A LEU* 5.7 1.8 - - - -
60A GLU* 2.9 37.8 + - + -
61A CYS 3.4 7.9 - - - +
62A PHE* 3.7 25.6 - - + -
67A GLY 3.5 2.8 + - - -
68A GLN* 1.3 81.0 - - - +
70A CYS* 1.3 64.2 + - - +
120A CYS* 3.4 39.4 + - + +
122A GLU* 3.9 20.1 + - - +
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Residues in contact with CYS 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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43A TYR* 4.0 16.4 - - + -
50A LEU* 4.8 0.3 - - - +
60A GLU* 3.6 5.9 - - - +
61A CYS* 2.8 36.9 + - - +
63A HIS* 4.7 2.5 - - - -
68A GLN* 3.6 22.9 - - - -
69A LYS* 1.3 81.5 - - - +
71A ALA* 1.3 61.2 + - - +
101A LEU* 3.6 24.5 - - - -
117A ILE* 3.8 13.0 - - + -
118A MET 3.4 12.8 - - - +
120A CYS* 4.0 12.0 - - - +
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Residues in contact with ALA 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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1A 05B 3.3 42.6 - - + +
50A LEU* 3.9 14.8 - - + -
58A VAL* 3.9 5.6 - - + -
59A LEU 3.3 4.5 - - - -
61A CYS* 4.4 1.1 - - - -
70A CYS* 1.3 75.3 - - - +
72A LEU* 1.3 61.1 + - - +
73A LYS 4.2 0.4 - - - -
116A ILE 3.7 0.7 - - - +
117A ILE* 3.4 5.0 - - - +
118A MET* 2.9 36.4 + - + +
119A GLU 4.3 0.4 - - - +
120A CYS* 4.3 1.2 - - - +
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Residues in contact with LEU 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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39A VAL* 4.3 15.0 - - + -
45A LEU* 3.7 39.0 - - + -
57A LYS 3.5 1.9 - - - +
58A VAL* 3.2 4.9 - - - -
59A LEU* 2.6 56.0 + - + +
61A CYS* 3.9 15.0 - - + -
71A ALA* 1.3 73.9 - - - +
73A LYS* 1.3 67.6 + - - +
74A LEU* 3.9 1.5 + - + +
115A LEU* 3.4 38.8 - - + -
116A ILE 3.4 11.7 - - - +
117A ILE* 4.1 7.2 - - + -
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Residues in contact with LYS 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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1A 05B 2.9 33.6 + - - +
53A GLY* 4.3 5.0 - - - -
54A VAL 5.0 0.6 - - - +
55A ASN* 4.8 1.2 - - - +
56A GLY* 3.6 31.0 - - - +
57A LYS 3.4 8.7 - - - +
58A VAL* 4.1 5.4 - - + +
72A LEU* 1.3 75.2 - - - +
74A LEU* 1.3 59.7 + - - +
75A LEU* 3.6 18.1 + - + +
84A GLU* 2.8 32.4 + - - +
114A LEU 3.5 1.2 - - - +
115A LEU* 3.4 4.9 - - - -
116A ILE* 2.8 39.5 + - + +
118A MET* 3.6 23.9 - - + +
187A ASP* 3.2 16.0 + - - -
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Residues in contact with LEU 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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55A ASN 3.5 1.0 - - - +
56A GLY* 3.0 27.0 - - - -
57A LYS* 3.0 44.9 + - + +
59A LEU* 5.5 11.0 - - + -
72A LEU* 3.9 2.5 + - + +
73A LYS* 1.3 69.8 - - - +
75A LEU* 1.3 77.1 + - - +
76A TYR* 3.8 26.2 - - + +
108A HIS* 4.2 25.8 - - + +
113A CYS* 4.4 4.7 - - - -
114A LEU 3.8 2.9 - - - -
115A LEU* 3.9 20.0 - - + -
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Residues in contact with LEU 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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55A ASN* 3.8 20.2 - - + +
56A GLY* 4.5 0.7 - - - -
73A LYS* 3.6 37.9 - - + +
74A LEU* 1.3 85.8 - - - +
76A TYR* 1.3 60.0 + - - +
81A ALA* 3.8 37.9 - - + +
84A GLU* 3.8 22.4 - - - +
85A VAL* 4.0 5.2 - - + -
113A CYS* 3.2 3.1 - - - -
114A LEU* 2.7 45.6 + - + +
116A ILE* 3.9 17.0 - - + -
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Residues in contact with TYR 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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55A ASN* 4.4 8.8 + - - +
57A LYS* 4.5 13.7 + - - -
74A LEU* 3.8 19.8 - - + +
75A LEU* 1.3 73.8 - - - +
77A ASP* 1.3 68.9 + - - +
78A SER* 3.7 3.8 + - - -
81A ALA* 3.3 14.0 - - - +
108A HIS* 3.6 22.5 + - - -
109A HIS* 5.2 4.0 - - - +
111A LYS* 3.7 33.3 - - + +
112A ARG 3.7 7.2 - - - +
113A CYS* 3.2 26.2 - - - -
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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