Contacts of the strand formed by residues 419 - 428 (chain B) in PDB entry 1ATT
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 ASN 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B TRP* 3.1 30.6 - - + -
53B SER* 3.5 16.4 + - - -
54B LYS* 4.4 4.9 - - - +
57B SER* 3.4 18.5 + - - -
305B LEU* 4.8 14.4 - - + +
309B LEU* 5.9 1.6 - - + -
414B ARG* 3.6 33.0 + - - +
415B GLU 3.0 7.5 + - - -
416B VAL 2.8 13.6 + - - +
417B ALA 3.6 0.2 - - - -
418B LEU* 1.3 85.0 + - - +
420B THR* 1.3 62.0 + - - +
421B ILE* 3.4 4.2 + - - +
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Residues in contact with THR 420 (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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53B SER* 4.2 10.0 - - - -
56B ASN* 5.5 4.9 - - - +
57B SER* 4.5 3.6 - - - -
82B LEU* 4.2 13.2 - - + -
127B LEU* 4.8 4.2 - - + +
131B LEU* 3.7 29.5 - - + +
414B ARG* 3.2 3.4 - - - +
415B GLU* 3.0 35.5 + - - -
418B LEU* 2.7 28.0 + - - +
419B ASN* 1.3 72.4 - - - +
421B ILE* 1.3 73.9 + - - +
422B ILE* 3.0 4.2 + - + +
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Residues in contact with ILE 421 (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 SER* 3.8 39.9 + - - +
60B ALA* 3.8 13.2 - - + -
61B THR* 4.0 15.0 - - + -
81B PRO* 4.1 14.9 - - + +
82B LEU* 4.0 12.8 + - - +
412B LEU* 4.7 15.3 - - + -
413B ILE 4.6 1.1 - - - +
414B ARG* 4.0 14.4 - - - +
419B ASN 3.4 4.0 + - - +
420B THR* 1.3 71.9 - - - +
422B ILE* 1.3 61.2 + - - +
423B PHE 3.9 16.8 - - - +
424B MET* 4.1 25.6 - - + -
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Residues in contact with ILE 422 (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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80B SER* 2.8 23.0 + - - -
81B PRO* 3.2 9.6 - - - +
82B LEU* 3.9 19.2 + - + -
131B LEU* 5.7 0.7 - - + -
141B LEU* 3.6 39.5 - - + -
220B ILE* 4.3 11.2 - - + -
280B ILE* 3.9 18.4 - - + -
413B ILE* 3.2 9.0 + - + +
414B ARG* 3.9 5.8 - - - +
415B GLU* 3.8 31.0 - - + +
420B THR* 3.0 9.9 + - + +
421B ILE* 1.3 72.3 - - - +
423B PHE* 1.3 81.9 + - + +
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Residues in contact with PHE 423 (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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78B PHE* 3.4 31.6 - + + -
79B LEU 3.7 4.9 - - - +
80B SER* 3.7 14.8 - - - -
81B PRO* 4.1 0.9 - - - -
141B LEU* 4.5 0.9 - - + -
220B ILE* 4.1 17.5 - - + -
222B PHE* 4.0 21.1 - + + -
372B ALA* 5.8 0.2 - - + -
383B ALA* 3.8 22.2 - - + -
384B ALA* 3.6 30.7 - - - -
385B ALA* 3.8 7.6 - - + -
412B LEU* 3.2 3.3 - - - -
413B ILE* 2.8 50.7 + - + +
421B ILE* 3.9 4.2 - - - +
422B ILE* 1.3 95.8 - - + +
424B MET* 1.3 61.9 + - - +
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Residues in contact with MET 424 (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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60B ALA 4.7 4.7 - - - +
61B THR* 4.0 25.6 - - + -
64B TYR* 3.9 38.1 - - + -
78B PHE* 3.2 8.0 - - - -
79B LEU* 3.0 37.0 + - + +
81B PRO* 4.3 13.7 - - + +
300B LEU* 4.3 20.6 - - + -
410B LEU* 6.0 0.9 - - + -
411B VAL 3.5 12.3 - - - +
412B LEU* 3.8 23.6 - - + +
421B ILE* 4.1 19.1 - - + -
423B PHE* 1.3 75.7 - - - +
425B GLY* 1.3 63.1 + - - +
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Residues in contact with GLY 425 (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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64B TYR* 4.1 10.1 - - - -
77B ILE 2.9 14.6 - - - -
78B PHE* 3.8 3.1 - - - -
326B ILE* 5.4 0.2 - - - -
410B LEU* 3.5 9.7 - - - +
411B VAL* 2.8 45.9 + - - +
424B MET* 1.3 79.5 - - - +
426B ARG* 1.3 58.3 + - - +
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Residues in contact with ARG 426 (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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64B TYR* 3.1 14.8 + - - +
68B ALA* 3.5 20.2 + - - +
71B LYS* 4.3 5.7 - - - +
72B ASN 3.9 15.4 + - - -
73B ASN* 4.3 16.6 - - - +
75B ASP 2.9 29.9 + - - +
76B ASN* 3.4 4.3 - - - +
77B ILE* 2.8 51.6 + - + +
293B LEU* 3.6 24.5 - - + -
297B GLU* 2.9 34.5 + - - -
326B ILE* 4.1 2.8 - - - +
408B PRO* 5.4 0.2 - - - -
409B PHE 3.6 5.8 - - - -
410B LEU* 4.2 3.4 - - + +
425B GLY* 1.3 71.9 - - - -
427B VAL* 1.3 64.4 + - - +
428B ALA* 4.1 12.3 - - + -
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Residues in contact with VAL 427 (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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76B ASN* 3.3 12.6 - - - +
240B PHE* 4.4 0.9 - - - -
324B PHE* 4.0 12.8 - - + -
326B ILE* 3.7 30.0 - - + +
408B PRO* 3.1 22.4 - - - +
409B PHE* 3.0 50.9 + - + +
411B VAL* 5.2 3.8 - - + +
425B GLY 4.2 0.6 - - - -
426B ARG* 1.3 72.6 - - - +
428B ALA* 1.3 62.0 + - - +
429B ASN 3.8 0.7 - - - +
430B PRO* 3.7 27.4 - - + -
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Residues in contact with ALA 428 (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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73B ASN 4.2 4.5 - - - +
74B ASN* 4.1 30.7 - - - +
75B ASP 4.1 2.0 - - - +
76B ASN* 2.8 6.3 + - - +
240B PHE* 3.5 11.0 - - - -
242B LYS* 4.1 9.4 - - - +
243B ALA* 4.4 1.1 + - + -
408B PRO* 3.4 31.0 - - + +
426B ARG* 3.7 19.4 + - - -
427B VAL* 1.3 76.7 - - - +
429B ASN* 1.3 61.4 + - - +
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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