Contacts of the strand formed by residues 59 - 67 (chain A) in PDB entry 1N3G
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 GLY 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASN* 3.7 4.9 + - - -
56A THR* 2.7 33.1 + - - +
58A ASN* 1.3 82.9 - - - +
60A VAL* 1.3 71.9 + - - +
88A LEU* 5.5 2.2 - - - -
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Residues in contact with VAL 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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53A THR* 3.6 31.4 - - + -
54A ILE 2.9 22.4 - - - +
55A ASN* 3.4 18.4 - - - +
56A THR* 3.5 4.2 - - - +
59A GLY* 1.3 81.7 - - - +
61A LEU* 1.3 60.1 + - - +
62A VAL* 3.3 15.4 + - + +
84A GLN* 4.0 6.7 - - - +
88A LEU* 5.4 2.9 - - - +
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Residues in contact with LEU 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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32A THR* 3.7 17.0 - - + +
34A LEU* 4.9 5.4 - - + -
52A ALA 3.0 6.1 - - - +
54A ILE* 2.7 38.6 + - + +
56A THR* 3.5 32.6 - - + +
60A VAL* 1.3 67.5 - - - +
62A VAL* 1.3 60.7 + - - +
81A LEU* 3.2 32.4 - - + +
84A GLN* 3.0 31.6 - - - +
85A LEU* 3.5 36.8 - - + +
88A LEU* 4.9 4.9 - - + -
89A GLN* 5.8 0.4 - - - +
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Residues in contact with VAL 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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51A ASP* 5.6 4.9 - - + -
52A ALA 3.2 9.4 - - - +
53A THR* 3.6 27.6 - - + +
60A VAL* 3.3 16.8 + - + +
61A LEU* 1.3 70.3 - - - +
63A ALA* 1.3 62.8 + - - +
64A SER* 3.6 17.2 + - - +
80A LYS* 5.8 1.6 - - - +
81A LEU* 3.4 5.3 + - - +
84A GLN* 3.5 11.3 + - - +
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Residues in contact with ALA 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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50A ALA 2.7 23.0 - - - +
51A ASP* 3.7 0.3 - - - -
52A ALA* 2.6 29.6 + - + -
62A VAL* 1.3 70.8 - - - +
64A SER* 1.3 54.2 + - - +
77A LEU* 3.3 43.9 - - + +
81A LEU* 3.2 28.8 - - + +
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Residues in contact with SER 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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50A ALA 3.4 4.5 - - - -
51A ASP* 5.0 7.6 - - - +
62A VAL* 3.6 16.9 + - - +
63A ALA* 1.3 71.8 - - - +
65A GLY* 1.3 59.3 + - - +
66A LYS 4.2 1.0 + - - -
77A LEU* 4.5 2.0 - - - -
80A LYS* 3.6 29.7 + - - +
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Residues in contact with GLY 65 (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 PHE 3.5 0.2 - - - +
50A ALA* 3.1 38.9 + - - +
63A ALA 3.9 0.6 + - - -
64A SER* 1.3 74.1 - - - +
66A LYS* 1.3 59.4 + - - -
73A ALA* 3.5 27.3 - - - +
76A GLU* 4.5 8.1 - - - -
77A LEU* 4.1 9.8 - - - +
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Residues in contact with LYS 66 (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 GLU* 3.8 19.8 + - - -
46A GLN* 4.6 13.2 + - - +
47A GLY 4.5 7.9 - - - +
48A PHE 3.1 19.5 - - - +
49A VAL* 3.8 26.9 - - + -
64A SER 4.2 1.0 - - - -
65A GLY* 1.3 73.1 - - - -
67A HIS* 1.3 75.7 + - - +
76A GLU* 5.5 3.2 - - - +
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Residues in contact with HIS 67 (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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46A GLN 5.7 0.2 - - - -
47A GLY* 3.7 2.9 - - - -
48A PHE* 2.6 40.8 + - - +
65A GLY 4.0 1.0 + - - -
66A LYS* 1.3 83.6 + - - +
68A GLU* 1.3 76.4 + - + +
69A ASP* 3.1 12.7 + - + +
72A THR* 3.0 41.9 - - + +
73A ALA* 4.3 6.0 - - - +
76A GLU* 5.0 8.9 - - + +
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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