Contacts of the strand formed by residues 171 - 182 (chain A) in PDB entry 1F5J
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASN* 3.6 21.8 - - - +
54A GLN* 3.4 32.5 - - - +
55A ASN* 4.2 6.8 + - - +
84A SER* 3.1 3.8 - - - -
85A THR* 2.8 52.1 + - - +
86A ASN* 4.3 4.2 + - - +
170A GLY* 1.3 71.7 - - - -
172A ILE* 1.3 60.7 + - - +
173A ASP* 3.4 1.7 + - - -
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Residues in contact with ILE 172 (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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52A TYR* 3.6 9.4 - - + +
53A ASN* 2.7 34.7 + - - -
54A GLN 2.9 18.5 + - - +
56A TRP* 3.6 31.9 - - + -
59A LEU* 3.8 12.6 - - + -
83A TRP 3.6 2.2 - - - +
84A SER* 4.3 6.7 - - - -
91A PHE* 4.2 11.0 - - + -
159A PHE* 4.0 16.8 - - + -
169A LEU* 4.2 13.2 - - + -
170A GLY 4.4 1.8 - - - +
171A THR* 1.3 72.1 - - - +
173A ASP* 1.3 55.5 + - - +
174A GLN 3.8 11.2 - - - +
175A ILE* 3.8 32.5 - - + -
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Residues in contact with ASP 173 (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 LYS* 3.4 19.0 + - - +
52A TYR 2.9 21.8 + - - -
53A ASN* 3.9 7.9 + - - +
83A TRP* 2.8 26.4 + - + +
85A THR* 4.8 7.5 - - + +
131A ILE* 4.0 20.9 - - + +
171A THR* 3.4 5.3 + - - +
172A ILE* 1.3 72.4 - - - +
174A GLN* 1.3 87.9 + - - +
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Residues in contact with GLN 174 (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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14A TYR* 4.0 12.4 + - + -
16A GLU* 5.2 0.2 + - - -
47A ARG* 3.0 41.2 + - - +
50A LYS 3.3 13.9 - - - +
51A LYS* 4.0 19.4 - - + +
52A TYR* 4.3 2.0 - - - -
81A TYR* 4.6 0.7 - - - -
82A GLY* 3.2 23.0 - - - -
83A TRP* 3.3 22.3 + - + +
91A PHE* 3.7 4.0 - - - -
131A ILE* 4.0 12.1 - - - +
172A ILE* 3.6 1.9 - - - +
173A ASP* 1.3 99.4 + - - +
175A ILE* 1.3 68.1 + - - +
176A THR* 3.9 11.4 + - + +
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Residues in contact with ILE 175 (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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50A LYS 3.0 29.6 + - - -
52A TYR* 3.7 29.4 - - + +
59A LEU* 4.9 0.4 - - + -
62A ILE* 3.9 20.0 - - + -
64A ILE* 3.7 26.0 - - + -
80A ILE* 3.8 15.5 - - + -
81A TYR 3.7 3.8 - - - -
82A GLY* 4.4 0.9 - - - -
91A PHE* 4.4 7.9 - - + -
155A VAL* 4.2 12.3 - - + -
159A PHE* 4.2 15.3 - - + -
172A ILE* 3.8 17.5 - - + -
174A GLN* 1.3 79.4 - - - +
176A THR* 1.3 63.1 - - - +
195A PHE* 3.4 8.7 - - + -
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Residues in contact with THR 176 (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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14A TYR* 4.7 7.4 - - + -
47A ARG* 3.3 30.5 - - + +
48A THR 3.3 14.1 - - - -
49A GLY* 3.8 14.6 - - - +
50A LYS 4.5 1.8 - - - +
64A ILE* 5.1 0.2 - - - -
80A ILE* 3.1 12.6 - - - +
81A TYR* 2.7 53.9 + - - +
174A GLN* 3.9 23.6 - - + +
175A ILE* 1.3 84.3 - - - +
177A LEU* 1.3 58.4 + - - +
195A PHE* 4.5 4.3 - - - -
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Residues in contact with LEU 177 (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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34A PHE* 3.8 5.7 - - + -
47A ARG* 3.3 3.1 - - - -
48A THR* 2.9 27.2 + - - +
66A TYR* 3.6 42.2 - - + -
67A SER 5.1 0.7 - - - +
78A LEU* 4.4 12.1 - - + -
79A CYS 3.5 15.7 - - - +
80A ILE* 3.9 17.9 - - + -
95A GLU* 6.2 1.3 - - + -
176A THR* 1.3 70.2 - - - +
178A CYS* 1.3 59.6 + - - +
190A ILE* 3.5 42.4 - - + -
192A GLN 3.7 3.6 - - - +
193A ASN* 3.5 26.3 + - - +
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Residues in contact with CYS 178 (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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34A PHE* 4.8 0.7 - - - -
45A LEU* 4.0 30.3 - - - -
46A PHE 3.3 10.5 - - - -
47A ARG* 3.6 13.5 - - + -
78A LEU* 3.5 6.1 - - - +
79A CYS* 2.6 48.3 + - - +
81A TYR* 3.7 28.3 - - + -
177A LEU* 1.3 75.5 - - - +
179A VAL* 1.3 76.8 + - - +
180A GLU* 4.2 3.1 - - - -
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Residues in contact with VAL 179 (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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34A PHE* 4.3 2.9 - - + -
36A CYS* 3.9 14.8 - - - -
38A TRP* 3.6 37.5 - - + -
45A LEU* 3.5 1.2 - - - -
46A PHE* 2.9 38.1 + - + +
70A TYR* 4.2 8.3 - - + -
77A TYR 3.4 7.2 - - - +
78A LEU* 4.0 11.2 - - + -
178A CYS* 1.3 77.1 - - - +
180A GLU* 1.3 62.5 + - - +
188A ALA* 3.9 11.7 - - + -
190A ILE* 3.7 30.7 - - + -
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Residues in contact with GLU 180 (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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38A TRP* 5.0 0.4 - - - -
43A ASN* 3.2 22.5 + - - +
44A ALA 3.3 12.6 - - - +
45A LEU* 3.7 23.3 - - + +
46A PHE* 6.0 0.2 - - - -
76A SER* 2.6 29.1 + - - -
77A TYR* 2.9 45.2 + - + +
79A CYS* 5.3 0.4 - - - -
92A TYR* 2.6 40.4 + - + -
178A CYS* 4.1 4.8 - - - -
179A VAL* 1.3 77.2 - - - +
181A GLY* 1.3 61.4 + - - +
182A TYR* 5.7 1.8 - - + +
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Residues in contact with GLY 181 (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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38A TRP* 4.0 15.6 - - - -
41A ILE* 3.4 16.6 - - - +
43A ASN* 3.0 22.6 + - - -
44A ALA 2.9 18.8 + - - -
46A PHE* 5.8 0.6 - - - -
75A ASN 3.6 7.4 - - - -
76A SER* 4.1 1.6 - - - -
180A GLU* 1.3 76.5 - - - +
182A TYR* 1.3 60.7 + - - -
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Residues in contact with TYR 182 (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 ILE* 3.8 0.2 - - - +
42A ASN* 3.1 37.1 + - - -
43A ASN* 4.1 17.9 - - + +
75A ASN* 3.0 52.3 + - - +
77A TYR* 6.0 2.7 - - + +
180A GLU* 5.7 1.8 - - + +
181A GLY* 1.3 73.7 - - - -
183A GLN* 1.3 105.8 + - + +
184A SER* 3.1 3.4 + - - -
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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