Contacts of the strand formed by residues 76 - 85 (chain D) in PDB entry 4QAE
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 CYS 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D VAL* 5.1 0.7 - - + -
70D MET 3.7 0.7 - - - +
75D LYS* 1.3 87.5 - - - +
77D GLU* 1.3 60.8 + - - +
78D TYR* 3.7 34.4 + - + +
175D CYS* 2.0 57.4 - - + -
14T CYS* 3.5 29.4 - - - -
15T HIS* 3.8 10.2 + - + -
21T MET* 4.3 5.5 + - - +
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Residues in contact with GLU 77 (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 ILE 3.3 3.6 - - - +
69D VAL* 3.3 4.3 - - - +
70D MET* 2.8 51.3 + - + +
72D LEU* 3.7 27.8 - - + +
75D LYS* 4.0 20.4 + - - -
76D CYS* 1.3 72.3 - - - +
78D TYR* 1.3 63.9 + - - +
79D LEU* 3.7 31.8 - - + +
75F LYS* 2.8 36.7 + - - +
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Residues in contact with TYR 78 (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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67D THR* 4.4 8.3 - - + -
68D ILE 3.3 4.7 - - - -
69D VAL* 3.8 34.3 - - + -
76D CYS* 3.7 23.2 - - + +
77D GLU* 1.3 75.3 + - - +
79D LEU* 1.3 67.4 + - - +
80D PHE* 3.6 29.2 - - + -
175D CYS 4.7 4.2 + - - -
127E TRP* 4.5 0.3 - - - -
14T CYS* 3.6 25.3 - - - +
21T MET* 3.6 19.3 - - + -
22T CYS* 3.6 0.5 - - - -
23T CYS* 3.1 62.5 + - + -
25T THR* 5.1 2.0 - - - -
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Residues in contact with LEU 79 (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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66D VAL 3.8 0.2 - - - +
67D THR* 3.5 4.7 - - - +
68D ILE* 2.7 47.0 + - + +
70D MET* 4.5 9.9 - - - -
77D GLU* 3.7 31.4 - - + +
78D TYR* 1.3 81.3 - - - +
80D PHE* 1.3 65.4 + - - +
75F LYS* 5.5 2.7 - - - +
9S PHE* 3.8 30.1 - - + -
20S GLY* 3.9 17.9 - - - -
21S MET* 3.9 28.5 - - + +
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Residues in contact with PHE 80 (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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66D VAL 3.3 3.8 - - - +
67D THR* 3.6 33.7 - - + -
78D TYR* 3.6 32.3 - - + -
79D LEU* 1.3 78.1 - - - +
81D GLN* 1.3 70.2 + - - +
21S MET* 4.9 12.5 - - - +
3T HIS* 3.8 19.3 - + + +
5T PRO* 3.8 38.8 - - + -
23T CYS* 5.4 3.4 - - + -
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Residues in contact with GLN 81 (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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65D ASN* 3.8 2.4 - - - +
66D VAL* 2.8 36.9 + - + +
68D ILE* 3.4 22.0 - - + +
79D LEU* 6.3 0.4 - - + -
80D PHE* 1.3 80.6 - - - +
82D THR* 1.3 63.7 + - - +
83D PHE* 3.3 31.2 - - + -
94D LEU* 3.7 27.6 - - + +
123D PHE* 5.5 1.9 - - - -
8S ILE* 5.4 0.2 - - - +
9S PHE* 3.3 45.0 + - + +
21S MET* 5.9 0.7 - - + -
3T HIS* 5.3 2.1 - - - -
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Residues in contact with THR 82 (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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63D SER* 4.3 12.3 - - - +
64D TYR 3.3 9.2 - - - +
65D ASN* 3.6 14.9 + - - +
81D GLN* 1.3 75.3 - - - +
83D PHE* 1.3 64.6 + - - +
84D VAL* 3.7 22.0 - - + -
94D LEU* 3.6 7.6 - - - +
95D GLY 3.1 39.5 + - - +
3T HIS* 5.9 0.3 - - - -
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Residues in contact with PHE 83 (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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54D THR* 5.6 0.9 - - + -
56D TYR* 3.4 41.7 - + - -
63D SER* 3.2 5.4 - - - -
64D TYR* 2.8 46.2 + + + -
66D VAL* 3.7 17.9 - - + -
81D GLN* 3.3 32.3 - - + -
82D THR* 1.3 78.3 - - - +
84D VAL* 1.3 61.2 - - - +
85D PRO* 3.9 0.3 - - - +
92D PHE* 3.8 20.4 - + + -
93D THR 3.6 3.4 - - - -
94D LEU* 3.7 22.7 - - + -
108D VAL* 3.9 23.8 - - + -
123D PHE* 3.9 19.7 - + - -
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Residues in contact with VAL 84 (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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63D SER* 4.1 6.7 - - - -
82D THR* 3.7 21.1 - - + -
83D PHE* 1.3 76.7 - - - +
85D PRO* 1.4 73.1 - - + +
92D PHE* 3.2 2.2 - - - -
93D THR* 2.8 60.5 + - - +
95D GLY* 4.0 19.1 - - - -
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Residues in contact with PRO 85 (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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61D ASP 4.4 4.3 - - - +
62D LYS* 3.5 37.5 - - + +
63D SER* 3.6 10.5 - - - +
83D PHE 3.9 0.7 - - - +
84D VAL* 1.4 87.4 - - + +
86D GLY* 1.3 68.2 + - - +
88D GLN 5.9 0.7 - - - +
89D PRO* 6.5 1.3 - - + -
91D GLU 3.6 1.3 - - - +
92D PHE* 3.5 17.2 - - + -
93D THR* 5.3 0.3 + - - -
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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