Contacts of the strand formed by residues 67 - 71 (chain D) in PDB entry 6H7L
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 PHE 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 4.3 0.7 - - - -
48D VAL* 3.5 19.5 - - + -
59D TYR* 3.4 16.7 - - + -
63D VAL* 3.0 43.3 + - + +
65D GLY* 4.8 3.8 + - - -
66D ARG* 1.3 106.1 + - + +
68D THR* 1.3 65.7 + - - +
80D LEU* 4.0 12.6 - - + -
81D GLN 3.4 4.0 - - - +
82D MET* 3.6 51.6 - - + -
83D ASN 3.9 2.9 - - - -
85D LEU* 3.7 17.7 - - + -
89D ASP* 3.9 16.8 - - - -
93D TYR* 3.8 10.5 - - - -
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Residues in contact with THR 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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59D TYR* 3.5 10.2 + - - +
65D GLY 6.0 0.3 - - - -
66D ARG 4.5 3.9 + - - -
67D PHE* 1.3 77.8 + - - +
69D ILE* 1.3 68.1 + - - +
70D SER* 4.2 6.3 + - - -
79D TYR 3.6 1.4 - - - +
80D LEU* 3.5 5.1 - - - +
81D GLN* 2.8 48.4 + - + +
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Residues in contact with ILE 69 (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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34D MET 3.9 2.9 - - - +
35D GLY* 4.2 0.4 - - - -
36D TRP* 3.9 14.6 - - + -
49D ALA* 3.4 37.7 - - + +
50D ALA* 3.6 28.5 - - - +
51D ILE* 3.9 10.9 - - + +
57D THR* 4.0 12.3 - - + +
59D TYR* 2.9 33.1 + - + +
68D THR* 1.3 75.8 - - - +
70D SER* 1.3 67.7 + - - +
78D VAL* 3.7 24.2 - - + -
79D TYR 3.3 10.8 - - - +
80D LEU* 4.1 2.9 - - + -
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Residues in contact with SER 70 (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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19D ARG* 5.0 2.4 + - - -
51D ILE* 4.1 9.6 - - - -
68D THR* 4.9 6.8 + - - +
69D ILE* 1.3 78.0 - - - +
71D ARG* 1.3 62.6 + - - +
78D VAL* 3.5 5.1 - - - +
79D TYR* 2.8 47.8 + - - +
81D GLN* 6.2 0.2 - - - +
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Residues in contact with ARG 71 (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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32D ASN* 2.8 31.3 + - - +
34D MET* 3.3 34.8 - - - +
51D ILE* 3.7 31.7 + - + +
52D HIS 3.9 13.7 - - - -
53D SER* 3.6 27.0 + - - +
55D GLY* 6.0 0.7 - - - -
70D SER* 1.3 78.5 - - - +
72D ASP* 1.3 73.5 + - - +
73D ASN* 3.4 5.1 + - - +
75D ALA 5.2 1.4 + - - -
76D ASN* 4.1 17.8 + - - +
77D THR 3.4 11.4 + - - +
78D VAL* 4.4 3.8 - - + -
79D TYR* 4.6 4.9 - - - -
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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