Contacts of the strand formed by residues 47 - 56 (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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLU* 2.7 45.9 + - - +
45A PRO 3.3 2.8 + - - -
46A GLN* 1.3 77.7 - - - +
48A PHE* 1.3 61.9 + - - -
49A VAL* 4.1 0.2 - - - +
66A LYS* 4.5 3.0 - - - +
67A HIS 3.6 19.3 - - - -
68A GLU* 3.8 10.6 - - - +
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Residues in contact with PHE 48 (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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10A MET* 3.6 24.0 - - + -
16A ILE* 4.2 8.5 - - + -
41A LEU* 3.9 29.8 - - + -
42A SER 3.7 6.1 - - - -
43A LYS* 3.3 36.8 - - + -
44A GLU 4.1 0.2 - - - +
47A GLY* 1.3 73.2 - - - -
49A VAL* 1.3 58.5 + - - +
50A ALA 3.8 0.7 - - - -
65A GLY 3.5 0.7 - - - +
66A LYS* 3.1 30.7 - - - +
67A HIS 2.6 21.0 + - - +
68A GLU* 4.3 6.7 - - - +
70A MET* 3.0 51.4 - - + -
73A ALA* 3.8 12.3 - - + -
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Residues in contact with VAL 49 (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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40A ILE 3.3 6.2 - - - +
41A LEU* 4.6 0.9 - - - -
42A SER* 2.7 46.1 + - - +
44A GLU* 3.2 50.0 - - + +
48A PHE* 1.3 71.7 - - - +
50A ALA* 1.3 57.5 + - - +
51A ASP* 3.1 32.4 - - - +
65A GLY 5.2 0.2 - - - -
66A LYS* 3.8 17.3 - - + -
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Residues in contact with ALA 50 (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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40A ILE 3.9 2.7 - - - -
41A LEU* 4.6 12.3 - - + +
48A PHE 3.8 0.6 - - - -
49A VAL* 1.3 68.9 - - - +
51A ASP* 1.3 56.1 - - - +
63A ALA 2.7 22.9 - - - +
64A SER* 3.4 2.1 - - - -
65A GLY 3.1 35.8 + - - +
73A ALA* 3.7 21.7 - - + +
74A ILE* 4.9 1.1 - - + +
77A LEU* 3.2 24.0 - - + -
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Residues in contact with ASP 51 (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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8A LYS* 6.1 1.2 - - - +
38A HIS 3.6 0.2 - - - +
40A ILE* 2.7 65.1 + - + +
42A SER* 5.6 1.0 + - - -
49A VAL* 3.1 33.5 - - - +
50A ALA* 1.3 72.8 - - - +
52A ALA* 1.3 56.8 + - - +
53A THR* 3.8 3.8 - - - +
62A VAL* 5.6 5.8 - - + -
63A ALA 3.7 2.2 - - - -
64A SER* 5.0 7.9 - - - +
65A GLY 5.4 0.2 + - - -
77A LEU* 4.6 0.4 - - - -
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Residues in contact with ALA 52 (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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38A HIS 3.4 5.2 - - - -
39A ILE* 3.4 26.9 - - + +
50A ALA 3.6 0.2 + - - -
51A ASP* 1.3 70.5 - - - +
53A THR* 1.3 60.5 - - - +
54A ILE* 3.8 5.6 - - + +
61A LEU 3.0 6.9 - - - +
62A VAL* 3.2 2.5 - - - +
63A ALA* 2.6 47.2 + - + +
77A LEU* 3.5 27.1 - - + -
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Residues in contact with THR 53 (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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36A ASN 3.5 3.5 - - - +
38A HIS* 2.6 47.8 + - - +
40A ILE* 3.7 15.4 - - - +
51A ASP* 4.0 4.5 + - - +
52A ALA* 1.3 69.7 - - - +
54A ILE* 1.3 57.7 + - - +
60A VAL* 3.6 14.6 - - + -
61A LEU 3.8 1.3 - - - -
62A VAL* 3.6 31.1 - - + +
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Residues in contact with ILE 54 (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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24A LEU* 5.0 11.7 - - + -
27A LEU* 4.9 5.8 - - + -
34A LEU* 3.3 54.5 - - + -
36A ASN 3.8 2.2 - - - -
37A PRO* 3.9 21.1 - - + -
39A ILE* 4.8 7.0 - - + -
52A ALA* 4.4 8.7 - - + +
53A THR* 1.3 75.7 - - - +
55A ASN* 1.3 63.7 + - - +
56A THR 3.4 1.4 + - - +
60A VAL* 2.9 9.2 - - - +
61A LEU* 2.7 50.3 + - + +
81A LEU* 4.2 23.3 - - + -
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Residues in contact with ASN 55 (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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34A LEU* 4.1 0.2 - - - -
35A ILE* 3.1 38.7 + - + +
36A ASN* 3.2 41.2 + - + +
54A ILE* 1.3 72.2 - - - +
56A THR* 1.3 61.4 + - - +
59A GLY 3.8 3.5 + - - -
60A VAL* 3.4 26.9 - - - +
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Residues in contact with THR 56 (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* 3.1 28.3 - - - +
34A LEU 4.9 0.7 - - - +
35A ILE* 4.4 1.8 - - - -
54A ILE* 3.4 0.8 + - - -
55A ASN* 1.3 76.6 - - - +
57A PRO* 1.3 70.5 - - - +
58A ASN* 3.0 12.4 + - - +
59A GLY* 2.7 55.0 + - - +
60A VAL 3.5 6.1 - - - +
61A LEU* 3.5 28.1 - - + +
88A LEU* 4.7 8.0 - - + +
89A GLN* 5.4 2.3 + - - -
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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