Contacts of the strand formed by residues 301 - 311 (chain A) in PDB entry 1U5U
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 PHE 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.7 37.2 - - + -
85A PHE* 3.8 33.4 - - + +
86A PRO* 4.9 2.7 - - + -
272A GLN* 3.2 4.8 - - - -
273A ILE* 2.9 46.3 + - - +
275A ILE* 4.1 23.6 - - + -
299A PRO* 3.9 32.1 - - + -
300A TRP* 1.3 77.2 - - - +
302A ASP* 1.3 67.8 + - - +
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Residues in contact with ASP 302 (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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80A VAL* 3.6 30.3 - - + +
83A PRO* 5.1 1.2 - - - +
84A LYS* 5.2 1.4 + - - +
85A PHE* 3.7 9.7 - - - -
270A ARG* 3.1 38.9 + - - +
271A LEU 3.9 2.9 - - - +
272A GLN* 3.0 26.6 + - - +
300A TRP 4.2 1.0 + - - -
301A PHE* 1.3 72.2 - - - +
303A LEU* 1.3 60.8 + - - +
304A ALA 5.1 0.6 - - - +
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Residues in contact with LEU 303 (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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79A ILE* 3.4 14.6 - - + +
80A VAL* 3.0 21.7 + - - +
85A PHE* 3.6 22.7 - - + -
91A PHE* 3.6 43.3 - - + -
212A TYR* 3.7 31.4 - - + -
271A LEU* 2.7 43.9 + - + +
272A GLN* 4.1 0.9 - - - -
273A ILE* 4.1 17.5 - - + -
301A PHE 3.3 1.4 + - - -
302A ASP* 1.3 73.8 - - - +
304A ALA* 1.3 64.1 + - + +
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Residues in contact with ALA 304 (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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77A ILE* 3.9 15.0 - - + -
78A THR 3.2 17.0 - - - +
79A ILE* 3.5 20.4 - - + -
80A VAL* 3.9 8.9 - - - +
270A ARG* 3.8 2.1 - - - -
271A LEU* 2.9 38.6 + - + +
302A ASP* 3.9 1.4 - - - +
303A LEU* 1.3 85.8 - - + +
305A LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 305 (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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76A GLU 3.7 1.4 - - - +
77A ILE* 3.4 4.3 - - - +
78A THR* 2.8 42.9 + - - +
80A VAL* 4.9 2.3 - - + +
218A ASP* 5.0 4.0 + - - -
268A ASN* 3.7 37.7 - - + +
269A TYR 3.7 9.0 - - - +
270A ARG* 5.1 1.3 - - + +
304A ALA* 1.3 73.3 - - - +
306A VAL* 1.3 67.7 + - - +
307A SER* 4.6 7.4 - - - +
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Residues in contact with VAL 306 (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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76A GLU 3.7 3.4 - - - +
77A ILE* 4.4 20.9 - - + +
101A LEU* 4.4 7.6 - - + -
119A PHE* 4.5 7.4 - - + -
121A ILE* 4.6 16.4 - - + -
267A VAL 3.5 1.2 - - - +
268A ASN* 3.1 5.5 - - - +
269A TYR* 2.7 62.4 + - + +
271A LEU* 4.0 26.7 - - + +
305A LYS* 1.3 78.5 - - - +
307A SER* 1.3 61.6 + - - +
308A ILE* 4.0 17.9 - - + -
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Residues in contact with SER 307 (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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75A GLY* 3.0 3.1 - - - -
76A GLU* 2.8 40.5 + - - -
266A PRO* 3.7 14.6 - - - +
267A VAL 3.6 2.7 - - - -
268A ASN* 2.6 22.1 + - - -
305A LYS* 4.0 11.5 - - - -
306A VAL* 1.3 74.4 - - - +
308A ILE* 1.3 63.1 + - - +
309A LYS* 3.7 19.7 + - - +
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Residues in contact with ILE 308 (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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73A GLY* 3.7 35.2 - - - +
74A ILE 3.9 0.2 - - - +
75A GLY* 3.9 14.1 - - - +
99A ALA* 5.3 4.5 - - + +
100A ARG 5.2 1.6 - - - -
101A LEU* 3.6 38.6 - - + +
121A ILE* 5.6 0.4 - - + -
258A TYR* 3.7 25.6 - - - +
262A LEU* 3.4 16.2 - - + +
266A PRO* 3.1 4.2 - - - +
267A VAL* 2.8 32.3 + - + +
269A TYR* 3.8 9.2 - - + -
306A VAL* 4.0 11.0 - - + -
307A SER* 1.3 75.8 - - - +
309A LYS* 1.3 60.9 + - - +
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Residues in contact with LYS 309 (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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74A ILE 3.0 8.2 + - - +
75A GLY* 4.5 4.7 - - - -
76A GLU* 3.5 30.9 + - - +
262A LEU* 3.9 18.8 - - - +
266A PRO* 3.9 20.9 - - + +
307A SER* 3.7 26.9 - - - +
308A ILE* 1.3 79.0 - - - +
310A THR* 1.3 67.9 + - - +
311A PRO* 4.4 1.0 - - - +
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Residues in contact with THR 310 (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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73A GLY* 3.1 3.6 - - - -
74A ILE* 2.8 54.2 + - + +
262A LEU* 3.7 4.6 - - - +
309A LYS* 1.3 86.6 + - - +
311A PRO* 1.3 85.7 - - + +
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Residues in contact with PRO 311 (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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72A GLY 4.0 3.1 - - - +
74A ILE* 5.2 1.0 - - - +
259A VAL* 5.1 18.6 - - + -
262A LEU* 3.5 30.0 - - + +
263A GLN* 6.0 3.4 - - + -
309A LYS 4.4 1.8 - - - +
310A THR* 1.3 107.7 - - + +
312A LEU* 1.3 65.2 + - - +
313A SER 4.2 0.3 + - - -
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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