Contacts of the strand formed by residues 58 - 64 (chain A) in PDB entry 2N23
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 MET 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.2 27.1 - - + +
57A LYS* 1.3 77.2 - - - +
59A MET* 1.3 66.2 + - - +
90A SER* 3.5 5.5 - - - -
91A PHE* 2.9 42.0 + - + +
92A ASN* 3.3 31.0 - - + +
93A ASN* 3.6 13.7 - - - +
94A ARG* 4.2 17.5 - - + +
97A MET* 3.2 28.3 - - + -
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Residues in contact with MET 59 (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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50A ALA* 3.1 5.9 - - - -
51A THR* 3.0 44.4 + - + -
57A LYS* 4.1 17.3 - - + +
58A MET* 1.3 80.0 - - - +
60A LEU* 1.3 63.1 + - - +
88A MET* 3.5 32.1 - - + +
89A PHE 3.2 19.5 - - - +
90A SER* 2.9 32.5 - - - +
91A PHE 4.7 0.2 - - - +
97A MET* 3.2 8.4 - - - +
27B PHE* 4.8 7.9 - - + -
30B TRP* 3.9 20.2 - - + -
31B TRP* 3.5 13.0 - - + -
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Residues in contact with LEU 60 (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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48A LEU* 4.0 9.4 - - + -
49A GLN 3.0 24.9 - - - +
50A ALA* 3.6 2.5 - - + -
59A MET* 1.3 80.0 - - - +
61A ARG* 1.3 63.6 + - - +
88A MET* 3.4 6.1 - - - +
89A PHE* 2.8 48.7 + - + -
91A PHE* 3.5 23.8 - - + -
97A MET* 3.6 33.9 - - + +
100A ILE* 3.8 17.3 - - + -
101A LYS* 3.4 30.3 - - + -
104A LEU* 4.5 2.7 - - + -
31B TRP* 4.7 0.2 - - - -
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Residues in contact with ARG 61 (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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48A LEU* 3.1 26.5 - - - +
49A GLN* 2.6 57.8 + - + +
60A LEU* 1.3 74.3 - - - +
62A LEU* 1.3 65.2 + - - +
63A ILE* 4.0 13.5 - - + -
86A ARG* 3.4 43.1 - - + +
87A HIS 3.0 13.0 - - - +
88A MET* 3.8 19.9 - - + +
89A PHE* 3.8 4.4 - - - -
104A LEU* 4.6 1.6 - - - +
28B LEU* 3.8 16.4 - - - +
31B TRP* 3.6 59.9 - - + +
32B ARG* 6.3 0.4 - - - +
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Residues in contact with LEU 62 (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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27A LEU* 3.5 21.3 - - + -
40A VAL* 3.9 13.5 - - + -
42A LEU* 3.7 16.8 - - + -
45A ILE* 3.4 38.1 - - + -
47A LYS 4.1 0.2 - - - -
48A LEU* 4.7 0.9 - - + -
61A ARG* 1.3 70.5 - - - +
63A ILE* 1.3 61.7 + - - +
64A GLY 3.2 3.3 + - - -
86A ARG* 2.9 5.9 - - - -
87A HIS* 2.7 57.1 + - + -
89A PHE* 3.0 31.1 - - + -
104A LEU* 3.6 14.6 - - + -
108A ILE* 4.4 5.4 - - + -
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Residues in contact with ILE 63 (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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45A ILE* 3.0 3.8 - - - +
46A ASP* 2.6 37.8 + - + +
47A LYS* 2.7 48.0 + - + +
48A LEU* 3.9 7.0 - - - +
49A GLN* 3.7 28.7 - - + +
61A ARG* 4.3 5.6 - - + -
62A LEU* 1.3 70.3 - - - +
64A GLY* 1.3 52.2 + - - +
84A PRO* 3.5 30.3 - - + -
86A ARG* 3.6 33.7 - - + +
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Residues in contact with GLY 64 (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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44A THR 3.6 8.7 - - - -
45A ILE* 3.8 11.7 - - - -
46A ASP* 4.3 0.9 - - - +
62A LEU 3.2 4.0 + - - -
63A ILE* 1.3 77.0 - - - +
65A LYS* 1.3 68.7 + - - +
66A VAL* 4.2 0.3 - - - +
84A PRO* 3.8 16.8 - - - +
85A GLN* 2.7 33.4 + - - +
87A HIS* 6.0 0.9 - - - -
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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