Contacts of the strand formed by residues 52 - 62 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48L ILE* 3.5 6.6 - - - +
49L GLN* 3.2 35.7 + - + +
50L ASN* 2.9 17.1 + - + +
51L GLY* 1.3 77.7 - - - +
53L VAL* 1.3 69.2 + - + +
54L VAL 4.2 0.2 - - - -
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Residues in contact with VAL 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L GLU* 4.4 23.8 - - + +
47L GLU 3.5 8.7 - - - +
48L ILE* 4.7 8.5 - - + -
51L GLY 5.0 2.0 - - - +
52L GLU* 1.3 85.9 - - + +
54L VAL* 1.3 63.7 + - - +
55L ARG* 4.5 9.2 - - - +
56L LYS* 6.2 5.8 - - + -
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Residues in contact with VAL 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 5.4 1.3 - - - +
25L ARG* 3.9 11.9 - - - +
47L GLU* 2.8 44.4 + - + +
49L GLN* 3.6 41.5 - - + +
52L GLU 5.8 0.2 - - - -
53L VAL* 1.3 75.1 - - - +
55L ARG* 1.3 71.7 + - + +
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Residues in contact with ARG 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 3.9 28.3 - - - +
20K ARG* 5.3 0.6 - - - +
26K GLU* 3.7 26.9 + - - -
28K ARG* 5.6 2.8 - - - +
69K PHE* 3.0 39.4 - - - -
71K SER* 5.6 0.2 - - - -
46L GLU* 3.5 5.0 - - - +
47L GLU* 3.0 46.4 + - + +
53L VAL* 3.4 6.9 - - - +
54L VAL* 1.3 89.3 - - - +
56L LYS* 1.3 72.5 + - - +
57L VAL* 4.9 12.1 - - + +
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Residues in contact with LYS 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L ALA 3.6 5.4 - - - +
46L GLU* 2.8 40.8 + - + +
53L VAL* 6.2 5.8 - - + -
55L ARG* 1.3 83.4 - - - +
57L VAL* 1.3 74.6 + - - +
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Residues in contact with VAL 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 5.9 4.7 - - + -
69K PHE* 6.1 0.9 - - + -
71K SER* 3.3 26.9 - - - +
72K PRO 5.1 4.3 - - - +
27L PHE* 4.5 9.2 - - + -
44L ASP* 3.5 3.5 - - - -
45L ALA* 3.1 36.6 + - + +
46L GLU* 5.7 0.4 - - - -
55L ARG* 4.9 18.4 - - + +
56L LYS* 1.3 87.0 - - - +
58L GLY* 1.3 65.4 + - - +
59L SER* 4.0 5.2 - - - +
60L VAL* 3.7 25.4 - - + -
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Residues in contact with GLY 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K PRO* 5.3 7.0 + - - +
43L LEU* 3.4 3.8 - - - +
44L ASP* 2.6 34.2 + - - +
57L VAL* 1.3 73.5 - - - +
59L SER* 1.3 64.5 + - - +
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Residues in contact with SER 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K VAL* 5.2 9.9 - - - +
71K SER* 3.0 22.5 + - - -
72K PRO* 3.0 28.6 - - - +
41L VAL* 5.2 4.5 - - - -
42L LEU 3.0 15.5 - - - -
43L LEU* 3.6 15.5 - - - +
45L ALA 5.5 0.4 - - - +
57L VAL* 3.1 5.0 - - - +
58L GLY* 1.3 82.4 - - - +
60L VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 60 (chain L).
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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69K PHE* 4.2 12.8 - - + -
70K VAL 3.5 4.9 - - - +
71K SER* 3.4 23.1 - - - +
72K PRO* 5.1 0.4 - - - -
27L PHE* 3.7 35.0 - - + -
40L LEU 3.6 1.2 - - - +
41L VAL* 3.2 7.5 - - - -
42L LEU* 3.1 42.9 + - + +
45L ALA* 4.8 1.3 - - + -
57L VAL* 3.7 15.7 - - + -
59L SER* 1.3 85.3 - - - +
61L VAL* 1.3 66.5 + - - +
62L ILE* 3.9 11.5 + - + +
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Residues in contact with VAL 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K PRO* 4.1 27.4 - - + +
8K VAL* 4.0 26.9 - - + -
9K LEU* 4.1 29.8 - - + -
38K MET* 4.7 21.3 - - + +
69K PHE* 3.2 6.2 - - - +
70K VAL* 3.0 34.1 + - + +
39L ASN* 5.4 0.2 - - + -
40L LEU 3.3 8.5 - - - +
41L VAL* 4.5 4.3 - - + -
60L VAL* 1.3 76.5 - - - +
62L ILE* 1.3 61.1 + - - +
63L ARG 4.1 0.3 + - - -
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Residues in contact with ILE 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K VAL 3.7 8.1 - - - +
69K PHE* 4.4 8.5 - - + -
19L VAL* 4.2 16.8 - - + -
21L LEU* 4.0 14.8 - - + -
27L PHE* 4.1 25.8 - - + -
38L MET 4.5 0.2 - - - +
39L ASN* 3.3 5.9 - - - +
40L LEU* 2.9 39.1 + - + +
42L LEU* 4.2 22.2 - - + -
60L VAL* 4.4 13.5 - - + +
61L VAL* 1.3 77.5 - - - +
63L ARG* 1.3 75.4 + - - +
64L GLY* 4.2 0.2 - - - -
66L THR* 4.8 1.1 - - - -
67L VAL* 3.9 19.3 - - + -
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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