Contacts of the strand formed by residues 68 - 76 (chain I) in PDB entry 5C3I
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 GLY 68 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29I GLU* 3.7 7.1 - - - -
30I CYS 2.8 34.9 + - - -
67I ALA* 1.3 74.7 - - - +
69I ARG* 1.3 61.7 + - - -
70I HIS* 3.1 17.6 + - - -
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Residues in contact with ARG 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ASN* 3.2 33.7 - - - +
8I ASN* 5.9 1.0 - - - +
27I THR* 3.4 34.2 - - + +
28I PHE 3.5 4.5 - - - +
29I GLU* 3.5 25.3 + - - +
68I GLY* 1.3 69.3 - - - -
70I HIS* 1.3 66.5 + - - +
71I MET* 5.2 4.3 - - + -
101K GLY 5.8 0.2 + - - -
101N VAL* 6.1 3.1 - - - -
105N GLU* 3.2 34.0 + - - -
40O ARG* 5.6 8.7 - - - -
98O TYR* 5.2 16.0 - - - +
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Residues in contact with HIS 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ILE 3.9 0.2 - - - +
27I THR* 3.3 6.9 - - - +
28I PHE* 2.9 58.4 + + + +
30I CYS* 4.7 0.4 - - + -
65I VAL* 3.9 14.6 - - + -
66I PRO* 2.5 60.1 + - + +
67I ALA 4.0 4.3 + - - -
68I GLY 3.1 22.8 + - - -
69I ARG* 1.3 78.5 + - - +
71I MET* 1.3 63.7 + - - +
72I PHE* 6.1 0.2 - - + -
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Residues in contact with MET 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I GLU* 3.7 26.5 - - + +
26I ILE 3.3 5.8 - - - +
27I THR* 3.5 34.1 - - + +
69I ARG* 5.2 3.4 - - + -
70I HIS* 1.3 77.0 - - - +
72I PHE* 1.3 65.4 + - - +
105N GLU* 4.3 12.1 - - + +
39O ARG 5.4 1.1 - - - +
40O ARG 4.4 9.0 - - - +
41O GLY 4.0 15.3 - - - +
42O GLY* 3.6 25.6 - - - -
44O LYS* 5.7 2.2 - - - +
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Residues in contact with PHE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I GLU* 3.5 3.5 - - - +
26I ILE* 2.9 61.5 + - + -
28I PHE* 4.0 21.5 - + - -
40I TRP* 3.6 44.6 - + - -
60I VAL* 5.0 6.5 - - + -
62I VAL* 4.9 12.6 - - + -
71I MET* 1.3 76.5 - - - +
73I VAL* 1.3 73.4 + - - +
74I PHE* 3.9 26.8 + + + -
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Residues in contact with VAL 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I LEU* 3.8 19.5 - - + -
23I GLN* 5.1 5.6 - - + +
24I PHE 3.3 10.1 - - - +
25I GLU* 3.9 23.1 - - + +
72I PHE* 1.3 82.0 - - - +
74I PHE* 1.3 65.6 + - - +
75I GLN* 3.9 12.7 + - + +
44O LYS* 3.9 20.0 - - - +
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Residues in contact with PHE 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I PHE 3.3 3.5 - - - +
23I GLN* 3.6 1.7 - - - -
24I PHE* 2.8 39.7 + - + +
26I ILE* 4.0 22.7 - - + -
40I TRP* 3.2 46.4 - - + -
41I LYS 4.9 0.2 - - - -
42I ILE* 3.4 39.3 - - + -
58I ASP* 3.9 22.0 - - + -
59I SER* 4.5 0.7 - - - -
60I VAL* 3.6 32.1 - - + -
72I PHE* 3.9 20.9 + + + -
73I VAL* 1.3 73.5 - - - +
75I GLN* 1.3 72.0 + - - +
76I ALA 4.2 0.4 - - - -
97I ILE* 5.3 1.8 - - + -
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Residues in contact with GLN 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I PRO* 3.5 31.0 - - + +
22I PHE 3.0 12.1 - - - +
23I GLN* 3.6 31.1 + - + +
58I ASP* 3.8 10.0 - - - +
73I VAL* 3.9 10.6 + - + +
74I PHE* 1.3 81.8 - - - +
76I ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I PRO* 3.3 5.9 - - - +
22I PHE* 2.7 39.9 + - + +
42I ILE* 3.8 22.0 - - + +
57I LEU* 3.8 17.7 - - + -
58I ASP* 3.4 31.2 - - + +
74I PHE 4.2 0.8 - - - -
75I GLN* 1.3 73.9 - - - +
77I ASP* 1.3 60.9 + - - +
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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