Contacts of the strand formed by residues 67 - 73 (chain A) in PDB entry 2EA3
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 ASN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE 2.8 19.4 + - - +
2A ASP* 3.1 27.7 + - - +
3A VAL* 2.8 28.9 + - - +
65A GLY 4.7 3.0 + - - -
66A VAL* 1.3 75.2 + - - +
68A LEU* 1.3 62.0 + - - +
69A LEU* 3.7 11.8 + - + +
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Residues in contact with LEU 68 (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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3A VAL* 3.8 29.6 - - + -
22A ALA* 4.0 3.6 - - + -
23A VAL 3.5 11.2 - - - +
24A ASN* 5.1 0.2 - - - -
25A GLY* 4.1 7.9 - - - +
26A GLY* 3.5 41.1 - - - +
62A THR* 3.7 18.4 - - + +
66A VAL* 3.7 9.3 + - + +
67A ASN* 1.3 71.5 - - - +
69A LEU* 1.3 65.6 + - - +
181A ILE* 3.4 31.4 - - + +
183A THR 5.4 1.0 - - - +
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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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2A ASP* 3.9 31.2 - - + +
3A VAL 3.2 18.6 + - - +
4A ILE* 4.0 9.8 - - + -
22A ALA* 3.4 19.4 + - - +
67A ASN* 4.1 16.4 - - + +
68A LEU* 1.3 80.3 - - - +
70A ALA* 1.3 59.4 + - - +
71A GLN* 2.9 44.2 + - + +
181A ILE* 4.6 0.9 - - - -
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Residues in contact with ALA 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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22A ALA* 5.3 0.9 - - - -
68A LEU 4.3 0.4 + - - -
69A LEU* 1.3 69.6 - - - +
71A GLN* 1.3 62.0 + - - +
81A GLN* 3.3 13.5 - - - +
82A VAL* 2.9 33.9 + - - +
181A ILE* 3.3 30.4 - - + +
182A THR* 3.4 27.6 - - - +
183A THR* 3.7 7.8 - - - +
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Residues in contact with GLN 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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4A ILE* 3.8 8.5 - - + +
5A GLY* 2.9 21.0 + - - -
21A PHE* 5.8 0.9 - - - -
69A LEU* 2.9 41.9 + - + +
70A ALA* 1.3 83.4 - - - +
72A VAL* 1.3 66.5 + - - +
79A ARG* 3.5 43.2 - - + +
80A VAL 3.2 8.5 - - - +
81A GLN* 3.6 22.8 + - - +
82A VAL* 4.1 3.0 - - - +
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Residues in contact with VAL 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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4A ILE* 3.8 2.7 - - - -
5A GLY* 3.5 9.0 - - - +
21A PHE* 3.9 8.7 - - + -
71A GLN* 1.3 78.9 - - - +
73A ASN* 1.3 68.0 + - - +
74A ASN 3.4 0.3 + - - -
79A ARG* 3.3 4.1 - - - -
80A VAL* 2.8 32.8 + - + +
82A VAL* 3.7 20.4 - - + -
97A SER* 3.5 29.8 - - - -
103A TRP* 4.2 4.0 - - + -
140A SER* 3.6 27.6 - - - +
142A LEU* 3.8 23.1 - - + -
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Residues in contact with ASN 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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4A ILE* 3.4 10.5 - - + +
5A GLY 2.8 18.8 + - - +
7A ASN* 2.8 31.3 + - - +
72A VAL* 1.3 70.9 - - - +
74A ASN* 1.3 61.1 + - - +
75A TYR* 2.8 47.3 + - + -
76A SER 4.7 0.2 + - - -
78A GLY 3.6 4.5 - - - +
79A ARG* 3.5 23.0 + - - +
97A SER* 2.6 30.3 + - - -
103A TRP* 3.8 0.3 - - - -
191A SO4 4.0 15.9 + - - -
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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