Contacts of the strand formed by residues 40 - 49 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H LEU* 5.1 7.4 - - + -
19H VAL* 3.5 39.0 - - + -
31H LEU* 4.8 8.3 - - + -
33H GLY 3.6 4.3 - - - +
34H TYR* 4.0 15.0 - - + +
38H MET* 3.4 22.9 - - + +
39H ASN* 1.3 91.9 - - - +
41H VAL* 1.3 71.0 + - - +
42H LEU* 4.8 7.2 - - + -
60H VAL 4.2 0.2 - - - -
61H VAL* 3.2 9.2 - - - +
62H ILE* 3.0 39.4 + - + +
67H VAL* 4.2 10.5 - - + -
70H VAL* 3.7 21.3 - - + -
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 3.8 1.2 - - - +
32H ASP* 3.1 35.7 + - + +
33H GLY* 3.1 22.7 + - - +
40H LEU* 1.3 80.0 - - - +
42H LEU* 1.3 76.7 + - - +
43H LEU* 5.2 5.2 - - + -
59H SER* 5.2 1.6 - - - -
60H VAL 3.2 11.2 - - - +
61H VAL* 4.7 3.4 - - + -
3N PRO* 6.1 0.4 - - + -
4N ARG 4.5 0.7 - - - +
5N PRO* 3.5 38.4 - - + -
8N VAL* 3.9 29.6 - - + -
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H VAL* 4.0 15.9 - - + -
19H VAL* 4.2 18.8 - - + -
27H PHE* 3.8 29.2 - - + -
29H GLY 4.4 8.7 - - - +
30H THR 3.2 9.2 - - - +
31H LEU* 3.8 22.7 - - + +
40H LEU* 4.8 3.4 - - + -
41H VAL* 1.3 86.3 - - - +
43H LEU* 1.3 64.2 + - - +
45H ALA* 4.3 14.1 - - + -
59H SER* 3.0 26.9 - - - -
60H VAL* 3.1 23.5 + - + +
62H ILE* 4.3 11.9 - - + -
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H GLY* 3.7 1.6 - - - -
30H THR* 3.1 38.0 + - + +
32H ASP* 3.4 39.7 - - + +
41H VAL* 5.2 3.1 - - + -
42H LEU* 1.3 74.1 - - - +
44H ASP* 1.3 82.2 + - - +
45H ALA 3.0 3.7 + - - -
58H GLY 3.5 5.6 - - - +
59H SER* 3.7 23.6 - - - -
11N ARG* 6.3 0.9 - - - +
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Residues in contact with ASP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ARG 4.1 0.5 - - - +
29H GLY* 4.1 6.4 - - - -
30H THR* 4.8 4.4 + - - +
43H LEU* 1.3 83.8 - - - +
45H ALA* 1.3 58.1 + - - +
46H GLU* 5.4 1.7 - - - +
57H VAL 3.7 7.4 - - - -
58H GLY* 3.0 16.4 + - - +
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PHE* 4.2 17.0 - - + -
28H ARG 2.9 22.2 - - - +
29H GLY* 3.7 6.7 - - - -
42H LEU* 4.3 13.9 - - + -
43H LEU 3.2 4.0 - - - +
44H ASP* 1.3 77.8 - - - +
46H GLU* 1.3 63.7 + - - +
56H LYS* 3.6 5.0 - - - +
57H VAL* 3.2 36.6 + - + +
59H SER* 6.1 0.2 - - - -
60H VAL* 4.9 4.5 - - + -
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PHE* 3.2 12.2 - - - -
28H ARG* 2.9 50.9 + - + +
44H ASP 5.4 1.3 - - - +
45H ALA* 1.3 79.5 - - - +
47H GLU* 1.3 60.1 + - - +
48H ILE* 3.7 3.6 + - + +
53H VAL* 3.9 35.9 - - + +
55H ARG 3.4 4.0 - - - -
56H LYS* 2.7 38.0 + - + +
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ARG* 3.0 47.6 + - + +
26H GLU 3.6 8.3 - - - +
27H PHE* 4.3 26.0 - - + -
46H GLU* 1.3 71.6 - - - +
48H ILE* 1.3 59.5 + - - +
49H GLN 3.1 4.0 + - - +
53H VAL* 4.4 1.6 - - - -
54H VAL* 2.9 31.1 + - + +
55H ARG* 2.9 49.8 + - + +
20N ARG* 5.5 2.6 - - - -
69N PHE* 4.3 16.2 - - - -
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ARG* 4.2 1.2 - - - -
26H GLU* 2.8 53.1 + - + +
28H ARG* 3.6 46.9 - - + +
46H GLU* 4.6 9.6 - - + +
47H GLU* 1.3 70.6 - - - +
49H GLN* 1.3 58.0 + - - +
50H ASN 3.5 2.1 + - - -
51H GLY* 3.3 31.8 + - - +
52H GLU 3.6 5.2 - - - +
53H VAL* 4.1 19.5 - - + +
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Residues in contact with GLN 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ARG* 2.6 51.8 + - + +
47H GLU 3.1 4.2 + - - -
48H ILE* 1.3 68.5 - - - +
50H ASN* 1.3 79.2 + - + +
51H GLY 2.9 3.5 + - - -
52H GLU* 2.9 24.6 + - + +
54H VAL* 3.2 38.9 - - + +
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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