Contacts of the strand formed by residues 65 - 72 (chain A) in PDB entry 1F5F
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 ASP 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASP* 3.2 0.7 - - - +
60A THR* 2.9 40.5 + - - +
61A ASN* 2.8 25.7 + - - +
63A LYS 3.9 0.2 - - - -
64A ASP* 1.4 88.7 - - - +
66A TRP* 1.3 56.1 + - - +
81A HIS 3.1 5.6 - - - -
82A ASN* 3.9 9.6 - - + +
83A HIS* 3.0 15.3 - - - -
84A TRP* 4.7 2.4 - - - -
136A HIS* 3.5 3.7 + - - -
251A ZN 2.2 36.4 - - - -
253A DHT 3.5 13.9 + - + +
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Residues in contact with TRP 66 (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 TYR* 3.7 22.7 - + + +
58A GLY 3.3 8.5 - - - +
59A ASP* 3.8 1.6 - - + -
61A ASN 3.9 0.9 - - - +
62A PRO 3.7 18.3 + - - -
63A LYS 3.9 14.1 + - - -
65A ASP* 1.3 77.0 - - - +
67A PHE* 1.3 69.5 + - - +
68A MET* 4.2 3.6 - - + -
79A GLN* 3.7 37.0 - - + -
80A LEU* 3.5 4.3 - - - +
81A HIS* 2.8 63.5 + + + +
148A PHE* 3.7 23.5 - + - -
152A ASN 4.5 4.6 + - - -
153A LEU* 3.7 31.6 - - + -
154A ARG* 4.0 20.9 - - + -
253A DHT 3.8 6.6 - - - +
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Residues in contact with PHE 67 (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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56A PHE* 3.8 29.2 - + - -
57A TYR* 3.3 7.6 - - - -
58A GLY 2.8 36.3 + - - +
66A TRP* 1.3 78.2 - - - +
68A MET* 1.3 62.7 + - - +
69A LEU* 4.0 14.4 - - + -
78A ILE* 3.7 36.3 - - + -
79A GLN 3.4 12.8 - - - -
80A LEU* 4.1 20.4 - - + -
105A VAL* 3.9 9.6 - - + -
112A VAL* 4.1 13.7 - - + -
253A DHT 3.7 57.9 - - + -
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Residues in contact with MET 68 (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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54A VAL* 4.0 14.8 - - + -
56A PHE 3.6 10.5 - - - +
57A TYR* 4.8 0.2 - - + -
66A TRP* 4.2 12.1 - - + -
67A PHE* 1.3 80.9 - - - +
69A LEU* 1.3 61.0 + - - +
70A GLY* 3.4 33.2 - - - +
77A GLU* 3.7 11.7 - - + +
78A ILE* 3.2 8.7 - - - +
79A GLN* 2.7 72.3 + - + +
146A LEU* 3.7 28.5 - - + -
153A LEU* 4.5 6.1 - - + -
157A LEU* 4.5 11.2 - - + -
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Residues in contact with LEU 69 (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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44A PHE* 3.9 20.0 - - + -
55A ILE* 2.8 33.6 + - + -
56A PHE* 2.9 49.1 + - + +
67A PHE* 4.0 10.4 - - + -
68A MET* 1.3 76.9 - - - +
70A GLY* 1.3 65.0 + - - +
76A PRO* 4.4 12.6 - - + -
77A GLU 3.5 13.2 - - - +
78A ILE* 3.8 15.9 - - + -
103A VAL* 4.1 8.7 - - + -
105A VAL* 4.0 12.1 - - + -
114A LEU* 4.3 12.8 - - + -
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Residues in contact with GLY 70 (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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53A GLY 3.2 14.4 - - - -
55A ILE* 3.8 8.0 - - - +
68A MET* 3.4 10.8 - - - -
69A LEU* 1.3 80.2 - - - +
71A LEU* 1.4 66.7 + - - +
76A PRO* 3.2 8.1 - - - +
77A GLU* 2.8 34.5 + - - -
157A LEU* 5.3 0.9 - - - -
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Residues in contact with LEU 71 (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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46A VAL* 6.2 1.1 - - + -
48A THR* 3.9 19.1 - - + -
50A ASP 3.6 19.5 - - - +
51A PRO 3.5 15.0 - - - +
52A GLU* 3.2 8.2 - - - +
53A GLY 2.9 29.1 + - - +
55A ILE* 4.3 16.8 - - + +
70A GLY* 1.4 82.9 - - - +
72A ARG* 1.4 63.7 + - - +
74A GLY 3.8 15.9 - - - +
75A ARG 3.3 4.9 - - - +
76A PRO* 3.6 20.9 - - + -
77A GLU* 4.9 0.2 - - - -
95A LEU* 4.0 23.3 - - + -
96A ASP* 4.7 2.0 - - + -
157A LEU* 3.7 6.3 - - - +
161A LEU* 4.3 10.3 - - + -
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Residues in contact with ARG 72 (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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51A PRO 3.6 1.6 - - - -
52A GLU* 4.2 17.9 + - - +
70A GLY 4.2 0.2 - - - -
71A LEU* 1.4 75.5 - - - +
73A ASP* 1.4 88.4 + - - +
74A GLY 3.2 0.2 - - - -
75A ARG* 2.9 22.6 + - - +
77A GLU* 2.6 50.7 + - + +
79A GLN* 3.6 0.6 - - - +
155A LEU* 3.0 49.0 + - - +
156A PRO 3.0 18.0 + - - -
157A LEU* 3.8 19.9 - - + +
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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