Contacts of the strand formed by residues 52 - 62 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.3 5.7 - - - -
49C GLN 3.1 32.7 + - - +
50C ASN 3.5 2.2 + - - +
51C GLY* 1.3 76.4 - - - +
53C VAL* 1.3 72.7 + - - +
54C VAL* 3.3 5.7 + - + +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 3.7 42.4 - - + +
47C GLU 3.4 7.4 - - - +
48C ILE* 4.6 8.1 - - + +
51C GLY 4.0 2.8 + - - +
52C GLU* 1.3 80.7 - - - +
54C VAL* 1.3 61.7 + - - +
55C ARG* 3.9 15.5 - - - +
56C LYS* 4.5 9.2 - - + -
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ARG* 3.6 25.1 - - - +
47C GLU* 2.8 24.5 + - + +
48C ILE 4.7 0.4 - - - -
49C GLN* 3.9 30.5 - - + +
52C GLU* 3.8 15.7 - - + +
53C VAL* 1.3 73.6 - - - +
55C ARG* 1.3 65.2 + - + +
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Residues in contact with ARG 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.9 29.4 - - - +
26B GLU* 3.1 41.1 + - - -
69B PHE* 3.6 26.8 - - - -
27C PHE* 5.7 0.2 - - - -
45C ALA 4.1 0.2 - - - +
46C GLU* 3.4 3.6 - - - +
47C GLU* 2.9 44.7 + - + +
53C VAL* 3.5 6.3 - - - +
54C VAL* 1.3 86.2 - - + +
56C LYS* 1.3 78.0 + - - +
57C VAL* 4.3 17.3 + - + +
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ALA 3.5 5.2 - - - +
46C GLU* 3.4 36.5 + - + +
53C VAL* 4.5 9.4 - - + -
55C ARG* 1.3 83.7 - - - +
57C VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 6.0 2.9 - - + -
69B PHE* 5.9 2.7 - - + -
71B SER* 3.6 21.3 - - - +
72B PRO 5.6 2.5 - - - +
27C PHE* 4.4 8.7 - - + -
44C ASP* 3.6 3.8 - - - -
45C ALA 3.0 34.9 + - - +
55C ARG* 4.3 21.8 - - + +
56C LYS* 1.3 81.2 - - - +
58C GLY* 1.3 67.5 + - - +
59C SER 3.9 10.8 - - - +
60C VAL* 3.4 28.3 - - + -
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO 5.1 6.3 + - - -
43C LEU* 3.4 5.6 - - - +
44C ASP* 2.6 34.6 + - - +
57C VAL* 1.3 71.0 - - - +
59C SER* 1.3 60.3 + - - +
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 5.1 7.4 - - - +
71B SER* 3.0 25.3 - - - -
72B PRO* 3.6 21.5 + - - +
41C VAL* 5.2 6.1 - - - -
42C LEU 3.0 18.8 - - - -
43C LEU* 3.5 18.3 - - - +
45C ALA 5.6 0.2 - - - +
57C VAL* 3.2 4.4 - - - +
58C GLY* 1.3 77.1 - - - +
60C VAL* 1.3 64.4 + - - +
61C VAL* 5.9 0.2 - - - -
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 4.5 8.7 - - + -
70B VAL 3.6 5.4 - - - +
71B SER* 3.5 13.7 - - - -
72B PRO* 5.2 0.2 - - - -
27C PHE* 3.9 29.2 - - + -
40C LEU 3.6 0.5 - - - +
41C VAL* 3.2 7.0 - - - +
42C LEU* 2.9 56.2 + - + +
45C ALA* 4.7 2.0 - - + -
57C VAL* 3.4 24.5 - - + -
59C SER* 1.3 80.5 - - - +
61C VAL* 1.3 70.0 + - - +
62C ILE* 4.5 8.3 - - + -
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 4.0 27.1 - - + +
8B VAL* 3.7 34.5 - - + -
9B LEU* 4.8 16.8 - - + -
38B MET* 5.0 14.6 - - + +
67B VAL* 5.6 0.2 - - - +
69B PHE* 3.2 6.3 - - - -
70B VAL* 2.9 43.1 + - + +
72B PRO* 5.9 2.2 - - + -
39C ASN* 5.3 0.2 - - + -
40C LEU 3.2 9.2 - - - +
41C VAL* 4.6 4.5 - - + -
60C VAL* 1.3 77.6 - - - +
62C ILE* 1.3 65.0 + - - +
63C ARG* 4.0 0.7 + - - +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL 3.7 8.7 - - - +
69B PHE* 4.4 11.2 - - + -
19C VAL* 4.3 15.0 - - + -
21C LEU* 3.9 15.0 - - + -
27C PHE* 4.1 22.7 - - + -
38C MET 4.5 0.3 - - - +
39C ASN* 3.2 6.0 - - - +
40C LEU* 2.8 44.4 + - + +
42C LEU* 3.9 29.6 - - + -
60C VAL* 4.5 9.0 - - + -
61C VAL* 1.3 76.3 - - - +
63C ARG* 1.3 75.7 + - - +
66C THR* 4.6 1.3 - - - -
67C VAL* 3.7 20.2 - - + -
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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