Contacts of the strand formed by residues 73 - 78 (chain A) in PDB entry 2A4X
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 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.2 6.7 - - + -
71A HIS* 3.1 27.4 - - + +
72A ARG* 1.3 91.0 - - + +
74A ALA* 1.3 78.8 + - - +
75A ILE* 3.8 24.7 - - + -
121A ASN* 3.5 43.7 - - + -
122A VAL* 4.0 5.7 + - - +
209B ALA 3.0 15.7 - - - +
210B VAL* 4.1 1.6 - - + +
211B VAL* 4.6 1.8 - - - +
272B ARG* 4.0 12.3 - - + -
273B PHE* 3.4 64.6 - + + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A HIS* 4.8 2.0 - - + +
73A PHE* 1.3 80.6 - - - +
75A ILE* 1.3 64.5 + - - +
76A ALA* 4.1 0.6 + - - -
122A VAL* 3.2 26.2 - - + +
124A ASP* 3.5 20.2 - - - +
700A BLM 4.2 7.9 - - + -
207B LEU* 4.0 0.9 - - - +
208B PHE* 3.6 3.6 - - - -
209B ALA* 2.9 39.5 + - + +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.1 14.4 - - + -
22A TYR* 3.8 27.6 - - + +
49A LEU* 4.8 6.3 - - + -
73A PHE* 3.8 24.2 - - + -
74A ALA* 1.3 75.6 - - - +
76A ALA* 1.3 61.6 + - - +
77A PHE* 3.6 24.0 - - + -
121A ASN* 6.0 0.4 - - + -
122A VAL 3.1 9.3 + - - +
123A VAL* 3.2 14.4 - - + +
124A ASP* 2.9 21.4 + - - -
205B ILE* 4.0 20.0 - - + -
207B LEU 3.7 5.6 - - - +
208B PHE* 3.8 26.7 - - + -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA 4.1 0.6 - - - -
75A ILE* 1.3 73.4 - - - +
77A PHE* 1.3 63.2 + - - +
112A TYR* 4.7 3.1 - - - +
124A ASP* 3.4 24.5 - - + +
126A PHE* 3.9 19.5 - - + -
205B ILE* 3.9 3.1 - - - +
206B SER* 2.9 24.8 + - - -
207B LEU* 2.9 38.4 + - + +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 3.8 27.4 - + - -
25A LEU* 3.7 40.8 - - + -
27A VAL* 3.9 9.2 - - + -
75A ILE* 3.6 18.8 - - + -
76A ALA* 1.3 76.8 - - - +
78A GLU* 1.3 60.5 + - - +
79A PHE* 3.6 17.9 - - + -
123A VAL* 3.6 30.1 - - + -
124A ASP 2.8 12.3 + - - +
125A LEU* 3.6 2.5 - - + -
126A PHE* 2.9 30.6 + - - +
203B ALA* 4.7 1.8 - - + -
204B ARG* 3.4 7.9 - - - +
205B ILE* 3.4 37.9 - - + -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ALA 4.1 0.6 + - - -
77A PHE* 1.3 73.3 - - - +
79A PHE* 1.3 72.7 + - - +
126A PHE* 3.4 22.3 - - + +
128A PRO* 3.9 20.0 - - + +
700A BLM 3.6 26.1 + - - -
202B SER 3.6 1.9 - - - +
203B ALA* 3.3 6.2 - - - -
204B ARG* 2.8 65.5 + - + +
206B SER* 3.7 14.3 + - - -
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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