Contacts of the strand formed by residues 59 - 68 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D GLU 3.4 0.9 - - - +
55D ILE* 3.3 4.5 - - - -
56D ILE 2.9 33.5 + - - +
57D ASP* 3.1 18.0 + - - +
58D GLY* 1.3 82.6 + - - +
60D VAL* 1.3 63.7 + - - +
61D TYR* 3.5 23.6 + - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ARG* 3.7 22.0 - - - +
53D GLU* 3.5 35.4 - - + +
54D GLU 3.3 2.9 - - - +
55D ILE* 4.5 8.5 - - + -
58D GLY 4.8 4.7 - - - +
59D ASN* 1.3 75.5 - - - +
61D TYR* 1.3 74.5 + - - +
62D LYS* 4.2 13.2 + - + +
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Residues in contact with TYR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 3.1 4.0 - - - -
54D GLU* 2.7 44.0 + - + +
56D ILE* 3.7 33.8 + - + +
57D ASP* 6.1 0.3 - - - +
59D ASN* 3.5 42.2 + - + +
60D VAL* 1.3 78.9 - - - +
62D LYS* 1.3 62.8 + - - +
63D ARG* 3.5 35.3 + - - +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PRO* 5.1 2.8 - - - +
1005C GOL 3.3 8.3 + - - -
52D ALA 3.7 7.0 - - - +
53D GLU* 3.8 23.6 - - + +
60D VAL* 4.0 10.3 + - + -
61D TYR* 1.3 72.5 - - - +
63D ARG* 1.3 69.1 + - - +
64D GLY 5.1 0.9 - - - +
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.3 21.2 - - + +
27C LYS* 4.5 4.0 - - - +
33C GLU* 4.2 12.1 + - - -
75C PHE* 5.0 0.4 - - + -
77C SER* 3.1 17.2 + - - +
78C PRO 3.6 2.6 - - - +
80C PRO* 3.2 17.0 - - - +
1005C GOL 2.7 68.2 + - - -
52D ALA* 2.7 15.3 + - + +
54D GLU* 2.8 33.5 + - + +
56D ILE* 5.0 1.8 - - - +
61D TYR* 3.7 36.7 + - - +
62D LYS* 1.3 81.4 + - - +
64D GLY* 1.3 58.3 + - - +
66D MET* 4.1 23.3 - - + -
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Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PRO* 4.5 7.6 - - - -
50D GLU 3.6 0.5 - - - -
51D ASP* 3.2 17.7 + - - -
52D ALA* 2.8 36.4 + - - +
62D LYS* 3.9 1.4 - - - +
63D ARG* 1.3 75.3 - - - +
65D THR* 1.3 64.5 + - - -
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Residues in contact with THR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 4.1 16.4 - - - +
77C SER* 2.8 21.1 + - - -
78C PRO* 3.1 29.9 + - + +
48D LEU* 3.8 18.2 - - + -
49D LEU 3.4 4.0 - - - -
50D GLU* 3.7 23.7 + - - +
63D ARG 3.8 1.6 + - - -
64D GLY* 1.3 72.3 - - - -
66D MET* 1.3 62.9 + - - +
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Residues in contact with MET 66 (chain D).
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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75C PHE* 3.6 56.8 - - + -
76C ILE 3.5 4.5 - - - +
77C SER* 4.2 2.0 - - - +
78C PRO* 5.0 0.2 - - - -
34D ILE* 3.9 32.1 - - + -
47D LEU 3.7 0.9 - - - +
48D LEU* 3.6 5.9 - - - -
49D LEU* 2.8 44.0 + - + +
52D ALA* 4.0 20.4 - - + -
53D GLU 4.9 0.7 - - - +
54D GLU* 4.5 2.0 - - + -
63D ARG* 4.1 19.7 - - + -
65D THR* 1.3 77.9 - - - +
67D VAL* 1.3 62.9 + - - +
68D VAL* 3.8 16.7 + - + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 4.6 16.8 - - - +
16C LEU* 4.3 21.5 - - + -
45C VAL* 6.0 2.7 - - + -
75C PHE* 3.2 6.1 - - - +
76C ILE* 2.8 63.9 + - + +
78C PRO* 5.7 1.1 - - + -
46D ASN* 6.1 3.1 - - + -
47D LEU 3.4 9.0 - - - +
48D LEU* 4.7 4.0 - - + +
65D THR* 5.4 0.4 - - - +
66D MET* 1.3 74.1 - - - +
68D VAL* 1.3 66.6 + - - +
69D ARG* 4.4 6.0 + - + +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU 3.7 10.1 - - - +
75C PHE* 4.1 3.4 - - + -
26D VAL* 5.1 2.2 - - + -
28D LEU* 3.8 27.8 - - + -
34D ILE* 5.1 4.0 - - + -
46D ASN* 3.2 5.2 - - - +
47D LEU* 2.9 47.1 + - + +
49D LEU* 4.4 17.0 - - + -
66D MET* 3.8 26.9 - - + +
67D VAL* 1.3 79.1 - - - +
69D ARG* 1.3 74.9 + - - +
73D VAL* 4.1 7.6 - - + -
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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