Contacts of the strand formed by residues 49 - 58 (chain F) in PDB entry 3AOI
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 PRO 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F SER 3.4 4.9 - - - +
48F ILE* 1.4 88.9 - - + +
50F GLY* 1.4 57.4 + - - +
146F ARG* 5.2 20.0 - - + +
147F GLY 2.9 17.3 - - - +
148F VAL* 3.4 16.2 - - + -
173F PRO* 3.1 14.1 - - - +
205F VAL* 4.4 8.7 - - - +
213F GLN* 3.4 27.1 - - + +
217F ILE* 5.6 3.6 - - + -
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Residues in contact with GLY 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F PRO* 1.4 75.2 - - - +
51F THR* 1.3 66.3 + - - +
146F ARG* 2.9 14.4 - - - +
147F GLY 2.6 32.8 + - - -
171F PHE* 3.4 8.9 + - - -
173F PRO* 3.5 15.7 - - - -
204F SER* 4.5 4.7 - - - -
205F VAL* 5.6 0.9 - - - -
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Residues in contact with THR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLY* 1.3 81.5 - - - +
52F ALA* 1.3 65.9 + - - +
85F LEU 5.3 2.3 - - - +
86F VAL* 5.1 2.6 - - - +
87F VAL* 2.9 45.7 + - - +
89F PHE* 3.9 34.8 - - + +
144F VAL* 4.2 2.2 - - - -
145F ASP 3.1 9.0 - - - -
146F ARG* 4.8 2.0 - - + -
170F VAL* 3.3 12.0 - - - +
171F PHE* 3.7 5.3 + - - -
173F PRO* 4.9 0.8 - - - +
202F ASP* 5.4 3.3 - - - +
204F SER* 4.3 11.3 + - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F THR* 1.3 82.2 + - - +
53F VAL* 1.3 64.4 + - - +
54F THR* 3.1 14.1 + - - -
83F LYS* 6.0 0.7 - - + -
85F LEU 5.0 7.0 - - - -
87F VAL* 5.5 0.9 - - - -
144F VAL* 3.6 6.8 - - - +
145F ASP 3.3 17.0 + - - +
168F ASP 5.0 0.4 - - - +
169F ALA* 4.4 5.4 - - - -
170F VAL* 3.4 41.1 - - + +
171F PHE* 3.6 12.5 - - + -
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Residues in contact with VAL 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ALA* 1.3 71.1 - - - +
54F THR* 1.3 61.1 + - - +
55F SER 4.0 0.9 - - - +
56F VAL* 3.8 28.5 - - + -
82F LEU* 2.9 41.1 - - + +
83F LYS* 4.4 6.9 - - - +
85F LEU* 4.0 26.0 + - + +
87F VAL* 6.5 0.4 - - + -
142F VAL* 3.9 15.5 - - + -
143F ARG 3.5 11.7 - - - +
144F VAL* 4.6 4.9 - - + +
167F VAL* 3.5 19.3 - - + +
168F ASP 3.9 11.6 + - - +
169F ALA* 5.1 0.4 - - - -
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ALA 3.2 11.3 + - - -
53F VAL* 1.3 74.1 - - - +
55F SER* 1.3 55.3 + - - -
143F ARG* 2.7 16.3 + - - +
145F ASP* 3.2 34.7 + - + +
156F HIS* 4.1 12.8 - - + +
158F ILE* 2.8 58.4 - - + +
167F VAL 3.1 18.1 + - - +
168F ASP 6.0 0.2 - - - -
169F ALA* 5.8 2.0 - - + -
171F PHE* 4.9 9.8 - - + -
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Residues in contact with SER 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F VAL* 3.6 2.5 - - - +
54F THR* 1.3 80.9 - - - +
56F VAL* 1.3 69.9 + - - +
141F GLU 4.7 0.2 - - - -
142F VAL* 3.3 0.5 - - - -
143F ARG* 2.7 46.8 + - - +
158F ILE* 3.8 33.6 + - - +
160F ASP* 5.0 5.8 + - - +
164F ALA* 4.1 13.7 - - - +
165F ILE 3.9 10.7 + - - -
166F PRO* 4.1 2.2 - - - +
167F VAL* 4.2 1.8 - - - +
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Residues in contact with VAL 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F VAL* 3.8 7.9 - - + -
55F SER* 1.3 82.0 + - - +
57F TYR* 1.3 71.6 + - - +
58F ILE* 4.8 4.5 - - + -
79F ILE* 3.9 5.4 - - + -
82F LEU* 3.5 26.5 - - + -
140F MET* 4.2 12.6 - - - -
141F GLU 3.4 5.2 - - - +
142F VAL* 3.1 23.8 - - + -
164F ALA* 3.1 6.2 - - - +
165F ILE* 2.9 46.1 + - + +
167F VAL* 3.4 24.0 - - + -
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Residues in contact with TYR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 1.3 77.7 - - - +
58F ILE* 1.3 78.4 + - - +
59F GLU* 3.8 25.0 + - + +
61F VAL 4.2 2.2 + - - -
140F MET* 3.0 25.3 - - - -
141F GLU* 3.0 27.4 + - + +
161F ARG* 3.6 38.0 - - + +
163F ASN* 3.2 52.8 + - + +
164F ALA* 3.4 11.0 - - + +
165F ILE* 5.0 1.1 - - - -
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 4.8 5.6 - - + -
57F TYR* 1.3 84.4 - - - +
59F GLU* 1.3 67.7 + - + +
60F ASP* 4.3 4.7 - - + +
61F VAL* 3.3 38.4 + - + +
68F ILE* 3.3 33.0 - - + -
75F VAL* 5.2 10.5 - - + -
78F ILE* 5.6 4.7 - - + -
137F ARG 5.5 1.6 - - - +
138F LEU* 3.7 14.8 - - + -
139F ASN 3.6 9.0 - - - +
140F MET* 3.0 48.7 - - + -
165F ILE* 5.7 3.9 - - + +
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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