Contacts of the strand formed by residues 76 - 83 (chain F) in PDB entry 3ALQ
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 LEU 76 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE* 3.4 59.0 - - + -
74F VAL* 4.7 4.3 - - + -
75F LEU* 1.3 75.4 - - - +
77F THR* 1.3 60.5 + - - +
97F ILE* 3.3 4.3 - - - +
98F ARG* 2.8 46.4 + - + +
100F PRO* 3.5 31.2 - - + -
114F TRP* 3.6 6.3 - - + -
116F GLU* 4.1 8.1 - - + -
118F ILE* 3.8 3.6 - - - +
137F ASN* 3.7 1.1 - - - -
138F ARG* 3.8 25.4 - - + -
141F TYR* 4.2 12.8 - - + -
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Residues in contact with THR 77 (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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64F PHE* 4.0 3.4 - - - -
75F LEU 4.6 0.9 - - - +
76F LEU* 1.3 79.9 - - - +
78F HIS* 1.3 60.4 + - - +
79F THR* 4.3 8.1 + - - -
95F SER* 5.7 0.4 - - - -
96F ALA 3.5 7.4 - - - -
97F ILE* 4.0 22.7 - - + -
118F ILE* 4.4 2.0 - - - -
135F GLU 5.1 0.7 + - - -
136F ILE* 3.2 26.9 - - - +
137F ASN* 3.0 38.6 + - - +
106V LEU* 4.3 18.6 - - + -
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Residues in contact with HIS 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 5.6 0.2 - - + -
28F TRP* 5.3 0.7 - + - -
60F SER* 2.8 39.2 + - - -
62F VAL* 3.5 48.1 - - + +
77F THR* 1.3 73.4 - - - +
79F THR* 1.3 73.3 + - - +
80F ILE* 4.9 0.4 - - + -
96F ALA 3.1 31.5 + - - -
118F ILE* 3.9 19.0 - - + +
120F LEU* 3.3 26.5 - - + +
134F ALA* 4.0 19.7 - - + -
135F GLU 3.7 5.5 + - - -
136F ILE* 3.6 12.1 - - + +
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Residues in contact with THR 79 (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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146E GLU* 5.1 0.7 + - - -
77F THR* 4.8 6.8 + - - -
78F HIS* 1.3 78.5 + - - +
80F ILE* 1.3 70.6 + - - +
81F SER* 4.0 5.0 + - - +
92F ASN* 3.6 36.6 + - - +
94F LEU 3.5 12.1 - - - +
95F SER* 2.9 17.8 + - - -
120F LEU* 4.0 1.1 - - - -
133F SER 3.5 2.8 - - - +
134F ALA* 3.7 0.7 - - - -
135F GLU* 3.0 40.0 + - - +
109V GLN* 5.4 2.0 - - - +
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Residues in contact with ILE 80 (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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58F ILE* 4.1 20.2 - - + -
59F TYR 3.9 13.2 - - - -
60F SER* 3.5 32.3 - - - +
78F HIS* 4.9 0.7 - - + -
79F THR* 1.3 75.0 - - - +
81F SER* 1.3 63.3 + - - +
92F ASN* 3.9 0.5 - - - -
93F LEU* 2.9 40.0 + - + +
94F LEU* 2.9 37.9 + - + +
120F LEU* 3.9 9.1 - - + +
132F LEU* 5.0 3.4 - - + -
133F SER 3.4 10.8 - - - +
134F ALA* 4.5 4.0 - - + -
152F PHE* 4.0 15.5 - - + -
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Residues in contact with SER 81 (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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79F THR* 4.0 6.3 + - - +
80F ILE* 1.3 73.7 - - - +
82F ARG* 1.3 60.7 + - - +
83F ILE* 5.4 2.9 - - - +
90F PRO* 4.4 14.0 - - - +
91F VAL 3.1 25.8 - - - -
92F ASN* 3.8 11.9 - - - -
93F LEU* 4.4 2.9 - - - -
131F ARG 3.8 0.5 - - - +
132F LEU* 3.6 7.4 - - - +
133F SER* 3.3 44.0 + - - -
135F GLU* 4.6 5.7 + - - -
109V GLN* 4.9 3.3 + - - -
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Residues in contact with ARG 82 (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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34E ASN* 2.9 31.7 + - - +
81F SER* 1.3 73.3 - - - +
83F ILE* 1.3 64.9 + - - +
84F ALA* 3.3 28.6 + - - +
86F SER* 4.3 4.9 + - - -
89F THR 3.3 4.7 - - - +
91F VAL* 2.7 34.9 + - + +
93F LEU* 3.5 25.8 - - + -
124F PHE* 6.1 0.6 - - - +
125F GLN* 3.4 26.1 + - - +
126F LEU* 3.9 10.1 - - + +
127F GLU* 4.0 12.9 - - - +
130F ASP* 2.6 32.9 + - + +
131F ARG 3.5 7.2 - - - +
132F LEU* 4.0 8.5 - - + -
68V VAL* 5.9 4.2 - - - +
69V PRO* 6.3 0.8 - - - +
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Residues in contact with ILE 83 (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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47F GLN* 3.5 28.7 - - - +
81F SER* 5.4 2.7 - - - +
82F ARG* 1.3 73.4 - - - +
84F ALA* 1.3 62.0 + - - +
85F VAL* 3.9 0.3 + - - +
88F GLN* 4.2 13.0 - - + +
89F THR* 4.1 20.9 - - - +
90F PRO* 4.1 25.6 - - + -
129F GLY 4.3 2.4 - - - +
130F ASP* 3.7 1.9 - - - -
131F ARG* 2.9 67.1 + - + +
133F SER* 5.7 3.6 - - - +
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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