Contacts of the strand formed by residues 59 - 68 (chain E) in PDB entry 1I8F
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 ASN 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E GLU 3.5 0.5 - - - +
55E ILE* 3.3 6.1 - - - -
56E ILE 2.8 41.5 + - - +
57E ASP* 4.1 7.3 + - - -
58E GLY* 1.3 78.6 + - - -
60E VAL* 1.3 61.4 + - - +
61E TYR* 3.0 36.8 + - + +
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ARG* 4.3 15.0 - - - +
53E GLU* 3.5 39.9 - - + +
54E GLU 3.5 3.4 - - - +
55E ILE* 4.7 9.4 - - + -
58E GLY 4.2 7.2 - - - +
59E ASN* 1.3 79.4 - - - +
61E TYR* 1.3 67.6 + - - +
62E LYS* 3.9 9.3 + - + +
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Residues in contact with TYR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D GOL 3.4 33.1 + - - -
53E GLU* 3.2 3.1 - - - -
54E GLU* 2.9 39.4 + - + +
56E ILE* 3.8 33.6 + - + -
59E ASN* 3.0 40.1 + - + +
60E VAL* 1.3 77.0 - - - +
62E LYS* 1.3 62.3 + - - +
63E ARG* 3.5 29.6 + - - +
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Residues in contact with LYS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D PRO* 4.6 7.9 - - + +
51E ASP* 4.5 20.3 + - - +
52E ALA 3.8 6.1 - - - +
53E GLU* 3.1 27.4 + - + +
60E VAL* 3.9 7.8 + - + +
61E TYR* 1.3 71.8 - - - +
63E ARG* 1.3 71.8 + - - +
64E GLY 4.9 2.2 - - - +
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 3.5 26.2 - - + +
33D GLU* 4.4 4.2 + - - -
75D PHE* 5.1 0.2 - - + -
77D SER* 3.8 16.5 + - - +
78D PRO 3.7 10.9 - - - +
80D PRO* 3.3 24.9 - - - +
1004D GOL 3.0 27.9 + - - -
52E ALA* 2.7 14.9 + - + +
54E GLU* 2.6 40.6 + - + +
61E TYR* 3.7 29.9 - - - +
62E LYS* 1.3 84.0 + - - +
64E GLY* 1.3 59.3 + - - +
65E THR 3.6 4.9 + - - +
66E MET* 4.0 18.8 - - + -
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Residues in contact with GLY 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D PRO* 4.5 5.8 - - - +
50E GLU 3.7 0.3 - - - -
51E ASP* 3.2 14.6 + - - -
52E ALA* 2.8 40.9 + - - +
62E LYS* 3.8 2.8 - - - +
63E ARG* 1.3 77.6 - - - +
65E THR* 1.3 58.6 + - - -
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Residues in contact with THR 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D THR* 3.8 20.6 - - + +
77D SER* 3.0 19.6 - - - -
78D PRO* 3.2 22.2 + - - +
48E LEU* 3.6 25.6 - - + -
49E LEU 3.3 7.6 - - - +
50E GLU* 4.2 16.5 + - + +
63E ARG 3.6 2.5 + - - +
64E GLY* 1.3 69.8 - - - -
66E MET* 1.3 63.2 + - - +
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Residues in contact with MET 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 3.7 47.6 - - + -
76D ILE 3.4 5.8 - - - +
77D SER* 4.0 2.2 - - - -
34E ILE* 3.7 41.1 - - + -
47E LEU 3.5 1.2 - - - +
48E LEU* 3.5 5.6 - - - +
49E LEU* 2.8 43.7 + - + +
52E ALA* 3.9 18.2 - - + -
53E GLU 4.9 0.9 - - - +
54E GLU* 4.5 2.0 - - + -
63E ARG* 4.0 24.2 - - + -
64E GLY 5.1 0.2 - - - -
65E THR* 1.3 77.3 - - - +
67E VAL* 1.3 63.2 + - - +
68E VAL* 3.9 14.0 + - + -
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Residues in contact with VAL 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D THR 3.0 27.4 - - - +
12D LEU* 2.6 39.7 - - + +
15D THR* 4.8 8.0 - - + +
16D LEU* 4.1 16.2 - - + -
75D PHE* 3.1 6.6 - - - +
76D ILE* 2.7 60.8 + - + +
47E LEU 3.1 11.2 - - - +
48E LEU* 4.7 5.2 - - + -
65E THR* 5.3 0.4 - - - +
66E MET* 1.3 74.4 - - - +
68E VAL* 1.3 59.4 + - - +
69E ARG* 4.3 0.3 + - - +
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Residues in contact with VAL 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.9 1.8 - - - -
74D LEU 3.8 9.0 - - - +
75D PHE* 4.5 1.8 - - + -
26E VAL* 4.7 2.2 - - + -
28E LEU* 3.8 18.4 - - + -
34E ILE* 5.2 4.3 - - + -
45E VAL 3.8 0.3 - - - +
46E ASN* 3.0 7.6 - - - -
47E LEU* 2.7 55.3 + - + +
49E LEU* 4.1 17.9 - - + -
66E MET* 3.9 25.4 - - + -
67E VAL* 1.3 75.5 - - - +
69E ARG* 1.3 63.7 + - - +
70E GLY 3.3 0.2 + - - -
73E VAL* 3.6 27.6 - - + -
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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