Contacts of the strand formed by residues 73 - 84 (chain B) in PDB entry 6A5T
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 LYS 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B LEU 2.9 11.8 - - - +
59B ASP* 3.5 0.2 - - - -
60B GLN* 2.7 57.1 + - + +
64B HIS* 5.3 11.5 - - + +
66B ASN* 5.5 10.2 + - - +
71B ILE* 2.8 31.7 + - + +
72B ASN* 1.3 67.8 - - - +
74B ARG* 1.3 59.5 + - - +
75B TYR* 3.1 33.4 + - + +
123B MET* 3.6 9.9 - - + -
429B ILE* 5.2 4.7 + - + +
432B ASP* 4.3 15.9 + - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 5.1 6.1 - - + -
58B LEU 2.7 7.9 - - - +
59B ASP* 3.5 24.8 + - + +
72B ASN* 2.8 50.0 + - + +
73B LYS* 1.3 68.2 - - - +
75B TYR* 1.3 62.3 + - - +
76B GLU 3.4 1.8 + - - -
123B MET* 3.2 9.2 - - - +
124B PHE* 2.9 64.8 + - + -
126B SER* 2.8 24.0 + - - -
128B ASP* 3.8 11.7 + - - -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 3.5 3.4 - - - -
58B LEU* 2.8 35.9 + - + +
60B GLN* 5.7 0.2 - - - -
73B LYS* 3.1 33.6 + - + +
74B ARG* 1.3 69.3 - - - +
76B GLU* 1.3 59.9 - - - +
77B ILE* 3.9 2.5 - - + -
121B LYS* 4.1 26.9 - - + -
122B SER 3.5 0.9 - - - -
123B MET* 3.2 35.3 - - + +
425B MET* 3.7 14.3 - - + +
428B CYS 5.9 0.2 - - - -
429B ILE* 3.3 56.9 - - + +
432B ASP* 3.9 17.3 + - - -
435B PHE* 5.2 0.7 - + + -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 2.7 48.6 + - + -
56B LEU 3.5 14.1 - - - +
57B ILE* 4.5 8.8 - - + +
74B ARG* 3.4 0.9 + - + +
75B TYR* 1.3 71.8 - - - +
77B ILE* 1.3 61.3 + - - +
78B ARG* 3.8 5.0 + - + +
120B GLU 3.7 2.6 - - - +
122B SER* 2.9 49.6 + - - +
123B MET 5.6 0.2 - - - -
124B PHE* 3.2 46.4 + - + +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 3.3 3.8 - - - -
56B LEU* 2.9 44.6 + - + +
75B TYR* 3.9 1.3 + - + +
76B GLU* 1.3 74.9 - - - +
78B ARG* 1.3 63.1 + - - +
79B PHE* 4.0 15.3 + - + -
119B MET* 4.8 20.9 - - + -
120B GLU 3.7 5.8 - - - +
121B LYS* 4.5 16.4 - - + -
421B ILE* 4.7 14.1 - - + -
425B MET* 3.5 46.4 - - + -
435B PHE* 4.7 14.6 - - + -
437B LEU* 5.6 6.5 - - + -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO* 3.5 12.6 - - + +
55B ARG* 3.0 58.8 - - + +
76B GLU* 3.8 6.5 + - + +
77B ILE* 1.3 74.3 - - - +
79B PHE* 1.3 71.4 + - - +
120B GLU* 2.9 48.6 + - + +
122B SER* 5.8 1.6 - - - +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.8 22.2 - - + -
51B TRP* 4.4 8.5 + - - -
53B GLU* 3.5 24.5 - - + -
54B PRO* 2.9 19.9 + - + +
55B ARG 4.5 0.4 - - - -
56B LEU* 4.8 10.5 - - + -
77B ILE* 4.6 15.9 - - + -
78B ARG* 1.3 85.2 + - - +
80B GLY* 1.3 59.8 + - - +
117B LEU* 4.7 12.1 - - + -
118B ASP 3.9 12.1 - - - -
119B MET* 4.2 26.5 - - + +
120B GLU* 5.6 0.4 - - - -
414B PHE* 4.4 23.1 - + - -
417B LEU* 6.2 2.0 - - + -
418B THR* 3.9 32.8 - - + -
421B ILE* 5.9 4.3 - - + -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 4.9 0.7 + - - -
50B VAL* 4.0 11.4 - - - +
51B TRP* 4.2 11.4 + - - -
78B ARG 3.8 0.6 + - - -
79B PHE* 1.3 77.7 - - - +
81B LYS* 1.3 69.2 + - - +
82B ILE* 4.0 8.8 - - - +
117B LEU* 4.4 1.0 - - - +
118B ASP* 3.1 21.5 + - - -
120B GLU* 5.9 2.7 - - - -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 4.5 14.4 - - - +
51B TRP* 5.9 3.6 - - + -
80B GLY* 1.3 77.6 - - - +
82B ILE* 1.3 85.1 + - - +
83B TYR* 3.2 42.6 + - + +
116B TYR 4.1 0.3 - - - +
117B LEU* 3.9 1.2 - - - -
118B ASP* 3.1 41.1 + - - +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 4.4 14.8 - - + -
47B GLN* 4.0 25.6 + - + +
50B VAL* 3.7 27.1 - - + -
80B GLY 4.0 1.6 - - - +
81B LYS* 1.3 100.2 - - - +
83B TYR* 1.3 76.2 + - - +
84B LEU* 4.7 8.7 - - + -
115B VAL* 3.8 27.4 - - + -
116B TYR 3.6 3.1 - - - +
117B LEU* 3.4 24.9 - - + -
158B ILE* 6.3 0.7 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 3.2 50.2 + - + +
82B ILE* 1.3 76.4 - - - +
84B LEU* 1.3 68.3 + - - +
85B SER* 6.1 0.4 - - - +
115B VAL* 3.8 0.3 - - - -
116B TYR* 2.9 49.3 + - + +
118B ASP* 3.9 12.0 + - - -
155B LYS* 3.6 36.6 - - + +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET* 3.8 43.3 - - + +
46B ILE* 5.8 5.4 - - + -
82B ILE* 4.7 9.0 - - + -
83B TYR* 1.3 85.1 - - - +
85B SER* 1.3 66.4 + - - +
113B SER* 5.1 6.1 - - - +
114B PRO 3.3 20.4 - - - +
115B VAL* 3.5 26.0 - - + -
116B TYR* 6.0 0.9 - - - -
169B PHE* 5.3 21.0 - - + -
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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