Contacts of the strand formed by residues 52 - 62 (chain A) in PDB entry 1I5L
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 GLU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.6 3.1 - - - -
49A GLN 2.7 26.3 + - - +
50A ASN* 4.7 9.2 - - - +
51A GLY* 1.3 76.4 - - - +
53A VAL* 1.3 70.4 + - - +
54A VAL* 2.8 24.2 + - + +
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Residues in contact with VAL 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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46A GLU* 4.1 37.5 - - + +
48A ILE* 3.8 17.9 - - + +
51A GLY 4.2 0.8 + - - -
52A GLU* 1.3 71.6 - - - +
54A VAL* 1.3 60.8 + - - +
55A ARG* 4.0 11.4 - - - +
56A LYS* 4.7 10.3 - - + -
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Residues in contact with VAL 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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25A ARG* 5.1 2.5 - - - +
47A GLU* 2.7 30.9 + - + +
49A GLN* 3.2 44.2 - - + +
52A GLU* 2.8 27.9 + - + +
53A VAL* 1.3 73.0 - - - +
55A ARG* 1.3 64.8 + - - +
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Residues in contact with ARG 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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46A GLU* 3.0 6.9 - - - +
47A GLU* 2.7 54.4 + - + +
53A VAL* 3.6 5.5 - - - +
54A VAL* 1.3 82.5 - - - +
56A LYS* 1.3 72.2 + - - +
57A VAL* 4.5 14.9 - - + +
18G ILE* 3.1 47.9 - - - +
20G ARG* 4.6 5.1 - - - +
26G GLU* 2.9 28.0 + - - -
69G PHE* 3.8 23.9 - - - -
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Residues in contact with LYS 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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45A ALA 3.3 4.0 - - - +
46A GLU* 3.0 40.8 + - + -
53A VAL* 4.7 9.6 - - + -
55A ARG* 1.3 76.1 - - - +
57A VAL* 1.3 70.7 + - - +
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Residues in contact with VAL 57 (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 PHE* 4.7 6.7 - - + -
44A ASP* 3.4 3.1 - - - -
45A ALA* 2.8 51.4 + - + +
55A ARG* 4.5 23.3 - - + +
56A LYS* 1.3 82.6 - - - +
58A GLY* 1.3 66.4 + - - +
59A SER 3.9 9.2 - - - +
60A VAL* 3.6 26.9 - - + -
18G ILE* 6.0 2.2 - - + -
69G PHE* 5.7 2.2 - - + -
71G SER* 3.9 20.6 - - - +
72G PRO 5.5 1.8 - - - +
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Residues in contact with GLY 58 (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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43A LEU* 3.5 6.4 - - - +
44A ASP* 2.9 25.5 + - - +
57A VAL* 1.3 73.7 - - - +
59A SER* 1.3 66.4 + - - +
72G PRO 5.4 4.4 + - - -
74G PRO* 6.4 0.4 - - - +
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Residues in contact with SER 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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41A VAL* 5.5 3.8 - - - -
42A LEU 2.8 20.4 - - - -
43A LEU* 3.5 15.7 - - - +
44A ASP 4.4 0.2 - - - +
45A ALA 5.4 0.4 - - - +
57A VAL* 3.0 6.1 - - - +
58A GLY* 1.3 84.9 - - - +
60A VAL* 1.3 63.1 + - - +
8G VAL* 5.3 8.0 - - - +
71G SER* 3.2 21.8 + - - -
72G PRO* 3.3 23.8 - - - +
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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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27A PHE* 3.8 28.5 - - + -
40A LEU 3.6 0.7 - - - +
41A VAL* 3.2 7.7 - - - +
42A LEU* 2.9 50.2 + - + +
45A ALA* 4.5 0.7 - - + -
57A VAL* 3.6 17.9 - - + -
59A SER* 1.3 81.3 - - - +
61A VAL* 1.3 64.0 + - - +
62A ILE* 3.9 12.5 + - + -
8G VAL* 6.1 0.4 - - - -
69G PHE* 4.0 19.3 - - + -
70G VAL 3.7 3.6 - - - -
71G SER* 3.4 18.8 - - - -
72G PRO* 5.2 0.2 - - - -
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Residues in contact with VAL 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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39A ASN* 5.4 0.9 - - + -
40A LEU 3.3 6.7 - - - +
41A VAL* 4.0 9.4 - - + -
60A VAL* 1.3 76.0 - - - +
62A ILE* 1.3 62.1 + - - +
63A ARG* 3.8 0.7 + - - +
5G PRO* 4.0 28.0 - - + +
8G VAL* 3.9 27.6 - - + -
9G LEU* 4.8 14.8 - - + +
38G MET* 4.6 23.6 - - + +
67G VAL* 5.6 0.3 - - - +
69G PHE* 3.4 5.1 - - - -
70G VAL* 3.0 41.4 + - + +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.4 12.1 - - + -
21A LEU* 3.8 23.8 - - + -
27A PHE* 4.0 26.5 - - + -
39A ASN* 3.3 2.6 - - - +
40A LEU* 2.8 41.6 + - + +
42A LEU* 3.8 31.4 - - + -
60A VAL* 4.2 14.8 - - + -
61A VAL* 1.3 75.9 - - - +
63A ARG* 1.3 75.1 + - - +
64A GLY* 3.3 1.0 + - - -
66A THR* 4.7 1.1 - - + -
67A VAL* 4.0 10.1 - - + -
68G VAL 4.0 7.9 - - - +
69G PHE* 4.3 7.9 - - + -
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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