Contacts of the strand formed by residues 80 - 89 (chain A) in PDB entry 1AF6
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 ALA 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.5 3.2 - - - -
65A ALA 2.8 33.7 + - - +
78A ASP 3.6 1.2 + - - -
79A PRO* 1.3 73.5 - - - +
81A PHE* 1.3 60.5 + - - +
82A ARG* 3.2 14.8 + - + +
66B TYR* 6.1 0.2 - - - -
74B TRP* 3.5 52.7 - - + +
75B GLU 3.3 11.7 - - - +
76B ALA* 4.0 0.4 - - - +
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Residues in contact with PHE 81 (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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62A THR* 4.8 7.0 - - + -
63A ASN 3.9 2.9 - - - -
64A VAL* 3.8 23.8 - - + +
79A PRO 3.9 1.8 + - - -
80A ALA* 1.3 68.8 - - - +
82A ARG* 1.3 58.5 + - - +
83A GLU 3.9 9.0 - - - -
84A ALA* 3.7 30.7 - - + -
104A LYS* 3.0 27.3 + - - -
40B THR* 3.7 22.2 - - + -
42B ALA* 3.5 26.9 - - + -
44B LEU* 4.6 7.6 - - + -
66B TYR* 3.8 42.4 - + + -
68B VAL* 4.2 23.0 - - + +
73B ASP 3.9 1.3 - - - +
75B GLU 3.0 12.0 + - - +
77B THR* 4.7 0.9 - - + +
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Residues in contact with ARG 82 (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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41A TYR* 2.8 28.9 + - - -
43A GLU* 3.3 4.6 + - - -
63A ASN* 3.0 12.6 + - + +
65A ALA* 3.7 20.6 - - + -
80A ALA* 3.7 19.7 - - + +
81A PHE* 1.3 75.0 - - - +
83A GLU* 1.3 64.7 + - + +
104A LYS* 3.4 22.2 + - - +
105A ARG 4.3 1.4 + - - -
106A PHE* 3.5 25.1 - - + -
124A GLY* 5.7 1.0 - - - -
73B ASP* 2.7 55.4 + - - +
74B TRP* 3.7 16.6 - - + +
1D GLC 3.1 15.0 + - - -
2D FRU 3.0 38.8 + - - -
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Residues in contact with GLU 83 (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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45A LYS* 2.9 29.3 + - - -
61A ASP* 4.4 3.9 - - - +
62A THR* 3.2 9.6 - - - +
63A ASN* 2.9 50.9 + - + +
81A PHE* 3.7 8.3 - - - -
82A ARG* 1.3 82.6 - - - +
84A ALA* 1.3 63.0 + - - +
85A ASN* 4.1 9.2 + - - +
104A LYS* 3.4 8.5 - - - +
105A ARG* 3.8 6.2 - - - +
106A PHE* 2.9 55.7 + - + +
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Residues in contact with ALA 84 (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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60A PHE* 4.8 2.9 - - + -
61A ASP 3.3 8.7 - - - -
62A THR* 4.8 4.3 - - + -
81A PHE* 3.7 25.6 - - + -
83A GLU* 1.3 75.8 - - - +
85A ASN* 1.3 59.5 + - - +
103A GLY* 3.2 5.4 - - - -
104A LYS* 2.9 28.1 + - + +
7B ALA* 5.1 5.8 - - + -
9B SER* 3.4 5.8 - - - +
40B THR* 4.3 12.6 - - + -
417B MET* 3.7 15.0 - - + -
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Residues in contact with ASN 85 (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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59A TYR 3.8 0.2 - - - +
60A PHE* 3.5 5.1 - - - -
61A ASP* 3.1 43.1 + - - +
83A GLU* 4.1 10.3 + - - +
84A ALA* 1.3 75.7 - - - +
86A VAL* 1.3 64.8 + - - +
87A GLN* 3.0 33.7 + - - +
101A TRP* 5.0 1.1 - - + +
102A ALA 3.4 17.0 - - - +
103A GLY* 3.8 5.6 - - - +
104A LYS 3.0 22.2 + - - +
105A ARG* 3.7 23.7 - - + +
417B MET* 3.9 4.8 - - - +
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Residues in contact with VAL 86 (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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58A PHE* 3.7 30.5 - - + -
59A TYR 3.3 8.7 - - - +
60A PHE* 4.0 14.1 - - + -
85A ASN* 1.3 78.5 - - - +
87A GLN* 1.3 64.5 + - - +
88A GLY 4.1 0.2 - - - -
101A TRP* 3.3 23.9 - - - +
102A ALA 3.2 10.2 + - - -
361B PRO* 4.0 26.9 - - + -
363B ILE* 4.0 13.0 - - + +
417B MET* 3.8 31.9 - - + -
419B ILE* 4.3 5.8 - - + -
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Residues in contact with GLN 87 (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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58A PHE* 3.2 4.7 - - - -
59A TYR* 2.9 43.9 + - + +
61A ASP* 4.7 13.5 + - - +
85A ASN* 3.0 26.8 + - - +
86A VAL* 1.3 73.8 - - - +
88A GLY* 1.3 60.7 + - - +
89A LYS* 3.6 29.2 + - - +
99A THR* 4.0 12.7 - - + +
100A ILE 3.5 4.0 - - - -
101A TRP* 3.8 15.9 - - + -
105A ARG* 4.0 27.1 + - - +
130A GLU* 5.2 0.2 - - - +
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Residues in contact with GLY 88 (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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57A SER 3.5 6.1 - - - -
58A PHE* 4.1 8.1 - - - -
87A GLN* 1.3 70.1 - - - +
89A LYS* 1.3 59.8 + - - -
91A LEU* 3.6 25.7 + - - +
98A SER 4.0 0.9 - - - +
99A THR* 3.3 3.6 - - - -
100A ILE* 2.6 46.3 + - - +
363B ILE* 3.9 4.3 - - - +
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Residues in contact with LYS 89 (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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55A ASP 5.6 0.7 - - - +
56A LYS* 3.5 1.4 - - - -
57A SER* 2.8 59.5 + - - +
59A TYR* 3.8 21.9 - - + +
87A GLN* 3.6 39.8 + - - +
88A GLY* 1.3 70.8 - - - -
90A ASN* 1.3 78.4 + - + +
91A LEU* 3.3 5.8 + - - +
97A GLY 5.8 1.6 - - - +
98A SER 3.9 0.9 - - - +
99A THR* 3.6 22.9 - - - +
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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