Contacts of the strand formed by residues 40 - 49 (chain G) 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 LEU 40 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LEU* 4.0 28.3 - - + -
19G VAL* 3.8 26.2 - - + -
31G LEU* 4.3 15.7 - - + -
33G GLY 3.7 2.2 - - - +
34G TYR* 4.1 7.0 - - + -
38G MET* 3.5 15.0 - - + +
39G ASN* 1.3 81.9 - - - +
41G VAL* 1.3 69.9 + - - +
42G LEU* 4.3 2.9 - - + -
60G VAL 4.3 0.2 - - - -
61G VAL* 3.4 8.0 - - - +
62G ILE* 3.0 40.4 + - + +
67G VAL* 4.2 10.8 - - + -
70G VAL* 3.8 27.4 - - + -
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Residues in contact with VAL 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PRO* 3.6 37.0 - - + -
8F VAL* 3.9 25.6 - - + -
31G LEU* 3.7 2.4 - - - +
32G ASP* 2.8 49.8 + - + +
33G GLY* 3.2 21.4 + - - +
40G LEU* 1.3 80.9 - - - +
42G LEU* 1.3 71.9 + - - +
43G LEU* 5.3 4.3 - - + -
59G SER* 5.5 2.0 - - - -
60G VAL 3.3 9.0 - - - +
61G VAL* 4.8 3.1 - - + -
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Residues in contact with LEU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL* 3.9 27.4 - - + -
19G VAL* 4.4 9.6 - - + -
27G PHE* 3.8 31.4 - - + -
29G GLY 4.3 7.4 - - - +
30G THR 3.3 13.9 - - - +
31G LEU* 4.0 7.2 - - + -
40G LEU* 5.1 1.6 - - + -
41G VAL* 1.3 84.1 - - - +
43G LEU* 1.3 64.1 + - - +
45G ALA* 4.2 11.7 - - + -
59G SER* 2.9 8.7 - - - -
60G VAL* 2.8 50.5 + - + +
62G ILE* 3.8 21.1 - - + -
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ARG* 5.8 5.6 - - - +
29G GLY* 3.9 0.3 - - - -
30G THR* 3.0 41.8 + - + +
32G ASP* 3.6 34.1 - - + +
41G VAL* 5.3 2.5 - - + -
42G LEU* 1.3 75.7 - - - +
44G ASP* 1.3 83.3 + - - +
45G ALA* 3.5 0.8 + - - -
58G GLY 3.4 3.4 - - - +
59G SER* 3.4 24.5 - - - -
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Residues in contact with ASP 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ARG 4.1 0.3 - - - +
29G GLY* 3.9 7.4 - - - -
30G THR* 4.5 1.7 + - - +
43G LEU* 1.3 86.1 - - - +
45G ALA* 1.3 58.6 + - - +
46G GLU* 5.3 1.6 - - - +
57G VAL 3.4 8.3 - - - -
58G GLY* 2.5 22.5 + - - +
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Residues in contact with ALA 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G PHE* 4.1 16.8 - - + -
28G ARG 3.0 18.2 - - - +
29G GLY* 3.9 7.6 - - - -
42G LEU* 4.2 17.5 - - + -
43G LEU 4.6 0.4 - - - -
44G ASP* 1.3 76.3 - - - +
46G GLU* 1.3 65.0 + - - +
56G LYS* 3.3 4.0 - - - +
57G VAL* 2.8 43.9 + - + +
60G VAL* 4.5 1.1 - - + -
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G PHE* 3.4 9.7 - - - -
28G ARG* 3.1 47.3 + - + +
44G ASP 5.3 1.3 - - - +
45G ALA* 1.3 81.7 - - - +
47G GLU* 1.3 60.4 + - - +
48G ILE* 3.8 6.9 + - + +
53G VAL* 4.2 28.2 - - + +
55G ARG 2.9 10.3 - - - +
56G LYS* 3.2 35.0 + - + -
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Residues in contact with GLU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ARG* 4.3 8.1 + - - -
26F GLU* 5.6 1.4 - - - +
69F PHE* 4.2 23.2 - - - -
25G ARG* 3.0 39.2 + - + +
26G GLU 3.5 10.1 - - - +
27G PHE* 4.4 18.0 - - + -
46G GLU* 1.3 72.1 - - - +
48G ILE* 1.3 61.9 + - - +
53G VAL* 3.3 5.7 - - - -
54G VAL* 2.8 37.4 + - + +
55G ARG* 2.6 44.6 + - + +
57G VAL* 5.9 0.2 - - - +
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Residues in contact with ILE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLY 4.6 0.7 - - - +
25G ARG* 3.4 5.2 - - - +
26G GLU* 2.7 60.2 + - + +
28G ARG* 3.2 39.7 - - + -
46G GLU* 4.0 13.5 - - + +
47G GLU* 1.3 78.2 - - - +
49G GLN* 1.3 64.7 + - - +
50G ASN 4.1 1.2 + - - +
51G GLY* 4.0 15.0 - - - +
52G GLU 3.4 21.8 - - - +
53G VAL* 4.5 14.1 - - + -
54G VAL* 5.0 0.4 - - - -
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Residues in contact with GLN 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLY 5.7 1.8 - - - -
25G ARG* 2.7 59.4 + - + +
48G ILE* 1.3 73.0 - - - +
50G ASN* 1.3 78.3 + - + +
51G GLY 3.5 0.4 - - - -
52G GLU* 2.9 20.8 + - - +
54G VAL* 4.1 17.2 - - + +
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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