Contacts of the strand formed by residues 65 - 70 (chain D) in PDB entry 3UX9
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 65 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLN* 4.3 11.2 - - - -
50D LEU* 3.9 30.3 - - + -
51D ILE* 4.5 4.5 - - + -
57D ARG* 3.2 25.4 + - - +
61D VAL* 3.7 18.4 - - + -
62D PRO* 3.7 37.9 - - + +
63D ASP 2.9 5.8 - - - +
64D ARG* 1.3 105.3 - - + +
66D SER* 1.3 62.2 + - - +
76D LEU* 4.8 7.6 - - + -
77D ALA 3.5 2.5 - - - -
78D ILE* 3.5 37.0 - - + -
85D ASP* 4.0 11.0 - - - -
89D TYR* 4.3 4.0 - + - -
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 4.1 7.9 - - - -
55D ASN 5.5 1.3 - - - -
57D ARG* 5.4 0.2 - - - +
63D ASP 5.2 3.6 - - - -
64D ARG 4.6 2.0 + - - -
65D PHE* 1.3 75.8 - - - +
67D GLY* 1.3 62.9 + - - +
75D SER 3.8 0.5 - - - +
76D LEU* 3.4 7.6 - - - +
77D ALA* 3.0 49.4 + - - +
79D THR* 5.7 2.1 - - - +
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Residues in contact with GLY 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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38D TRP* 5.0 2.5 - - - -
51D ILE* 3.8 16.7 - - - +
54D ASN 3.1 21.5 - - - -
55D ASN* 3.3 20.7 + - - +
66D SER* 1.3 78.2 - - - +
68D SER* 1.3 62.1 + - - -
75D SER 3.6 6.1 - - - -
76D LEU* 4.9 2.0 - - - -
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Residues in contact with SER 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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38D TRP* 5.3 0.7 + - - +
54D ASN* 3.4 9.6 + - - +
55D ASN* 5.1 1.8 - - - -
67D GLY* 1.3 75.3 - - - -
69D LYS* 1.3 66.9 + - - +
70D SER* 5.1 4.0 - - - -
73D SER 5.5 0.2 + - - -
74D ALA* 3.3 6.6 - - - +
75D SER* 3.0 46.3 + - - -
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Residues in contact with LYS 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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35C ASP* 2.8 35.0 + - - +
31D ILE* 2.6 38.1 + - + +
32D GLY 3.8 10.1 + - - -
34D ASN 2.9 23.6 + - - -
36D VAL* 4.5 3.8 - - + -
54D ASN* 3.5 29.0 - - + +
68D SER* 1.3 77.4 + - - +
70D SER* 1.3 65.4 + - - +
71D GLY 4.3 11.2 - - - +
73D SER 3.6 10.5 - - - +
74D ALA* 4.8 1.1 - - + -
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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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68D SER* 5.1 4.5 - - - -
69D LYS* 1.3 76.4 - - - +
71D GLY* 1.3 54.9 + - - +
72D THR* 2.8 15.6 + - - +
73D SER* 2.9 26.5 + - - -
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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