Contacts of the strand formed by residues 67 - 78 (chain X) in PDB entry 2AT8
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 THR 67 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58X TYR* 3.8 29.4 - - + +
59X HIS 3.4 5.2 - - - +
60X TYR* 3.3 14.1 - - + -
65X GLN 2.8 19.4 + - - -
66X ASP* 1.3 76.3 + - - +
68X PHE* 1.3 73.9 + - - +
69X TYR* 4.5 10.5 - - + -
96X LYS* 5.9 1.6 + - - -
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Residues in contact with PHE 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X TYR* 3.6 15.7 - - - -
58X TYR* 3.6 2.6 - - - -
59X HIS* 2.9 66.8 + + + +
66X ASP* 3.3 26.9 - - - -
67X THR* 1.3 82.1 - - - +
69X TYR* 1.3 65.5 + - - +
70X ASP* 3.5 17.9 - - - -
88X LYS* 3.9 33.0 - - + +
89X VAL 5.3 0.4 - - - -
185X FDD 3.7 47.6 - + + -
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Residues in contact with TYR 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X LEU 3.2 15.7 - - - +
58X TYR* 3.4 39.7 - + + -
67X THR* 4.5 8.1 - - + -
68X PHE* 1.3 77.9 - - - +
70X ASP* 1.3 72.5 + - - +
88X LYS* 3.4 5.7 - - - +
89X VAL* 3.0 46.4 + - + +
90X ASP* 4.3 2.0 - - - +
91X LYS* 3.6 38.2 + - + -
174X ASP* 3.7 25.6 + - - +
177X SER* 4.4 8.3 - - - -
178X LEU* 4.2 11.9 - - + -
181X LEU* 3.5 21.3 - - + -
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Residues in contact with ASP 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X GLU 4.7 0.2 - - - -
56X ALA* 3.3 5.9 - - - +
57X LEU* 2.8 52.1 + - + +
59X HIS* 4.7 1.2 + - - -
68X PHE* 3.5 13.2 - - - +
69X TYR* 1.3 81.6 - - - +
71X VAL* 1.3 65.6 + - - +
86X PHE* 3.6 17.0 - - + -
87X LYS 3.2 14.1 - - - +
88X LYS* 3.5 2.8 - - - -
89X VAL* 4.1 1.8 - - - -
181X LEU* 4.6 1.6 - - - +
185X FDD 2.5 48.4 - - - +
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Residues in contact with VAL 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X LYS* 3.7 16.6 - - - -
55X GLU 3.8 4.0 - - - +
56X ALA* 4.6 0.7 - - + +
70X ASP* 1.3 76.4 - - - +
72X SER* 1.3 64.0 + - - +
73X GLU* 5.6 2.2 - - + -
85X ASN* 4.3 1.6 - - - +
86X PHE* 3.5 1.9 - - - -
87X LYS* 2.9 50.6 + - + +
89X VAL* 3.9 22.2 - - + +
99X VAL* 5.4 0.2 - - - +
181X LEU* 3.6 34.1 - - + +
182X LEU* 5.7 0.2 - - - -
184X LYS* 3.3 30.5 - - + +
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Residues in contact with SER 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X LYS* 3.3 11.9 - - - -
55X GLU 2.7 38.7 + - - +
57X LEU* 4.3 5.9 - - - +
71X VAL* 1.3 76.1 - - - +
73X GLU* 1.3 62.7 + - - +
74X LEU* 3.8 9.9 - - - -
85X ASN* 2.9 21.7 + - - -
86X PHE* 3.8 4.9 - - - +
105X TYR* 2.9 34.5 + - - -
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Residues in contact with GLU 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X LYS* 6.0 4.1 - - + +
53X LEU 3.7 6.1 - - - +
54X LYS* 4.0 19.4 + - + -
71X VAL* 5.6 1.8 - - + -
72X SER* 1.3 75.1 - - - +
74X LEU* 1.3 63.9 + - - +
75X GLN* 4.0 10.2 + - - +
83X THR 3.9 1.0 - - - +
84X ALA* 3.5 1.2 - - - -
85X ASN* 2.8 61.3 + - - +
87X LYS* 6.2 4.3 - - - -
99X VAL* 4.8 4.8 - - - +
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Residues in contact with LEU 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X PHE* 3.8 22.9 - - + -
53X LEU* 2.9 39.9 + - + +
54X LYS 4.3 0.7 - - - -
55X GLU* 3.8 41.7 - - + +
72X SER* 3.8 14.8 - - - -
73X GLU* 1.3 78.8 - - - +
75X GLN* 1.3 70.2 + - - +
76X VAL* 4.3 1.4 + - - +
82X TYR* 3.9 31.0 - - + -
83X THR 3.6 1.8 - - - -
84X ALA* 3.7 22.7 - - + -
107X PHE* 4.8 3.1 - - + -
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Residues in contact with GLN 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X GLU* 5.0 10.8 - - - +
74X LEU* 1.3 81.8 + - - +
76X VAL* 1.3 65.5 + - - +
77X GLU* 4.7 9.0 - - - +
82X TYR* 3.2 9.3 - - - +
83X THR* 2.9 39.6 + - - +
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Residues in contact with VAL 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X LEU* 4.5 10.5 - - + -
74X LEU 5.2 0.9 - - - +
75X GLN* 1.3 78.9 - - - +
77X GLU* 1.3 69.0 + - - +
78X SER* 3.6 26.2 - - - +
79X LEU* 4.7 2.2 - - - +
81X LYS 4.5 0.2 - - - +
82X TYR* 3.9 21.1 - - + -
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Residues in contact with GLU 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X GLN* 4.3 8.0 - - - +
76X VAL* 1.3 80.0 - - - +
78X SER* 1.3 65.6 + - - +
81X LYS* 2.9 30.0 + - + +
82X TYR 4.2 2.5 - - - +
83X THR* 2.6 40.6 + - - +
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Residues in contact with SER 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ALA* 5.7 0.7 - - - +
76X VAL* 3.6 14.6 - - - +
77X GLU* 1.3 80.2 - - - +
79X LEU* 1.3 70.2 + - - +
80X GLY 3.0 1.0 + - - -
81X LYS* 3.0 38.0 + - - +
82X TYR* 4.5 1.2 - - - -
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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