Contacts of the strand formed by residues 130 - 139 (chain A) in PDB entry 2E56
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A THR 4.3 0.2 - - - +
83A ASN* 2.7 41.0 + - - +
128A LYS 3.7 0.2 + - - -
129A GLY* 1.3 75.3 - - - +
131A TYR* 1.3 71.4 + - - +
132A LYS* 2.8 45.1 - - + +
152A VAL* 3.9 16.0 - - - +
153A ILE 3.7 3.8 - - - -
154A LEU* 3.6 26.4 - - + +
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Residues in contact with TYR 131 (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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54A LEU* 4.1 19.3 - - + -
80A ILE* 5.9 3.6 - - + -
81A THR 3.3 6.5 - - - +
82A VAL* 3.6 40.3 - - + +
83A ASN* 4.6 2.7 + - - -
124A ILE* 3.7 30.0 - - + +
127A SER* 2.9 32.8 + - - -
128A LYS 3.3 32.9 + - - -
129A GLY 4.5 1.1 - - - -
130A LYS* 1.3 79.2 - - - +
132A LYS* 1.3 62.8 + - - +
152A VAL* 3.5 3.1 - - - -
153A ILE* 2.7 59.0 + - + +
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Residues in contact with LYS 132 (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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79A TYR 4.4 0.4 - - - +
80A ILE* 3.3 6.6 - - - +
81A THR* 2.7 54.6 + - + +
130A LYS* 2.8 43.0 - - + +
131A TYR* 1.3 79.8 - - - +
133A CYS* 1.3 61.5 + - - +
134A VAL* 4.2 2.0 - - + +
150A GLU* 4.1 21.7 + - + +
151A PHE 3.2 7.2 - - - +
152A VAL* 4.1 16.6 - - + -
153A ILE* 4.7 2.0 - - - -
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Residues in contact with CYS 133 (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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78A LEU* 3.9 26.7 - - - -
79A TYR 3.4 3.8 - - - -
80A ILE* 3.8 24.9 - - + -
132A LYS* 1.3 75.6 - - - +
134A VAL* 1.3 65.7 + - - +
135A VAL* 4.1 1.8 - - - -
149A LEU 3.7 1.2 - - - +
151A PHE* 2.8 43.8 + - + +
153A ILE* 4.5 4.2 - - + +
701A MYR 3.8 32.3 - - + -
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Residues in contact with VAL 134 (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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37A CYS* 3.8 18.2 - - - -
77A ASN 3.3 7.1 - - - +
78A LEU* 3.5 2.8 - - - -
79A TYR* 2.9 52.8 + - + +
132A LYS* 5.7 2.0 - - + -
133A CYS* 1.3 74.7 - - - +
135A VAL* 1.3 63.4 + - - +
136A GLU* 4.6 4.9 - - + +
148A CYS* 3.9 8.1 - - - -
149A LEU 3.3 8.7 - - - +
150A GLU* 3.9 32.8 - - + +
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Residues in contact with VAL 135 (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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76A PHE* 3.8 41.5 - - + -
77A ASN 3.7 3.1 - - - -
78A LEU* 3.9 15.0 - - + -
133A CYS* 4.1 6.7 - - - -
134A VAL* 1.3 74.6 - - - +
136A GLU* 1.3 60.3 + - - +
137A ALA 3.6 1.0 + - - -
147A PHE* 3.9 15.1 - - + +
148A CYS* 3.3 4.3 - - - -
149A LEU* 2.7 37.5 + - + +
151A PHE* 3.8 31.0 - - + -
601A MYR 4.3 8.5 - - + -
701A MYR 4.3 5.6 - - + -
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Residues in contact with GLU 136 (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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75A TYR 3.5 1.2 - - - +
76A PHE* 3.3 5.1 - - - -
77A ASN* 3.0 62.3 + - + +
79A TYR* 4.0 19.2 + - + -
134A VAL* 3.9 4.9 + - + +
135A VAL* 1.3 70.9 - - - +
137A ALA* 1.3 61.4 + - - +
138A ILE* 3.6 13.3 + - + +
145A MET* 6.1 3.8 - - + -
147A PHE 3.9 5.4 - - - +
148A CYS* 4.6 15.3 - - + +
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Residues in contact with ALA 137 (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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74A LEU* 4.2 0.9 - - + -
75A TYR 3.5 4.7 - - - -
76A PHE* 3.6 15.5 - - + -
135A VAL 3.6 1.4 + - - -
136A GLU* 1.3 72.0 - - - +
138A ILE* 1.3 56.9 + - - +
145A MET* 3.7 2.3 - - - +
146A LEU* 2.7 40.9 + - + -
147A PHE* 2.9 57.0 + - + +
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Residues in contact with ILE 138 (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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74A LEU* 3.3 1.9 - - - +
75A TYR* 2.8 81.7 + - + +
77A ASN* 3.4 26.2 - - - +
136A GLU* 4.2 15.9 - - + +
137A ALA* 1.3 79.9 - - - +
139A SER* 1.3 66.2 + - - +
143A GLU* 3.7 28.3 - - + +
144A GLU 3.6 15.5 - - - +
145A MET* 4.8 5.6 - - + -
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Residues in contact with SER 139 (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 ARG* 4.5 6.0 - - - +
70A ASP 2.8 20.8 + - - -
71A LEU* 4.1 4.3 - - - -
72A LYS 3.9 3.1 - - - -
73A GLN* 4.6 2.0 - - - -
74A LEU* 3.7 26.7 - - - +
75A TYR* 5.8 0.4 - - - -
138A ILE* 1.3 80.0 - - - +
140A GLY* 1.3 58.9 + - - +
141A SER* 3.1 11.0 + - - -
142A PRO 3.4 0.5 - - - +
143A GLU* 3.5 2.9 - - - -
144A GLU* 3.3 29.3 + - - +
146A LEU* 4.1 20.2 - - - +
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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