Contacts of the strand formed by residues 96 - 104 (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 THR 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLU* 3.4 24.2 + - - +
77A ILE 3.0 5.8 - - - -
78A THR* 3.6 27.6 - - + +
94A GLY 3.7 6.3 - - - +
95A ARG* 1.3 86.1 - - - +
97A PHE* 1.3 68.2 - - - +
98A PRO* 4.6 2.1 - - - +
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Residues in contact with PHE 97 (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* 3.4 7.3 - - - +
77A ILE* 2.8 47.0 + - + +
79A ILE* 4.0 20.6 - - + -
90A PHE* 3.5 36.1 - + - -
95A ARG* 3.3 49.1 - - + -
96A THR* 1.3 77.7 - - - +
98A PRO* 1.3 79.1 - - + +
123A PHE* 3.6 45.8 - + + +
131A PRO* 4.6 4.5 - - + -
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Residues in contact with PRO 98 (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 3.8 6.5 - - - +
76A GLU* 4.8 2.5 - - + -
96A THR 4.6 2.0 - - - +
97A PHE* 1.3 90.0 - - + +
99A ALA* 1.3 60.4 + - - +
123A PHE 3.2 6.8 - - - +
124A ALA* 3.0 23.4 + - - -
125A ASP* 4.0 23.6 - - + +
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Residues in contact with ALA 99 (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* 3.1 10.4 - - - +
75A GLY 2.9 39.5 + - - +
76A GLU 4.7 0.2 - - - +
77A ILE* 3.6 29.8 - - + -
97A PHE 4.1 0.7 - - - +
98A PRO* 1.3 77.8 - - - +
100A ARG* 1.3 65.8 + - - +
121A ILE* 5.6 1.6 - - + -
122A LYS 3.2 15.0 - - - +
124A ALA 3.7 4.2 - - - -
125A ASP* 4.4 3.1 - - - +
306A VAL* 6.1 0.4 - - + -
308A ILE* 5.6 5.4 - - + -
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Residues in contact with ARG 100 (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 3.5 5.8 - - - +
74A ILE* 3.8 8.5 - - + +
99A ALA* 1.3 78.2 - - - +
101A LEU* 1.3 61.2 + - - +
120A SER 3.8 0.3 - - - +
121A ILE* 3.2 5.6 - - - +
122A LYS* 2.9 36.1 + - + +
124A ALA 3.7 8.6 + - - +
125A ASP* 2.8 30.7 + - - +
126A SER* 3.2 35.9 + - - +
127A ASP* 2.8 26.7 + - - +
308A ILE* 5.2 0.4 - - - -
312A LEU* 4.1 14.1 - - + +
316A VAL* 3.4 20.7 - - - +
317A LEU* 6.4 0.4 - - + -
320A THR* 2.8 38.0 + - + -
322A PHE* 3.9 9.7 - - + -
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Residues in contact with LEU 101 (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* 3.2 8.5 - - - -
73A GLY 3.0 31.4 + - - +
100A ARG* 1.3 77.1 - - - +
102A ARG* 1.3 72.8 + - - +
103A HIS* 3.5 29.4 - - + +
119A PHE* 3.3 37.9 - - + -
120A SER 3.1 11.2 - - - +
121A ILE* 3.8 7.2 - - + -
258A TYR* 4.1 8.3 - - + +
269A TYR* 3.8 9.9 - - + -
306A VAL* 4.4 0.9 - - + -
308A ILE* 3.6 33.7 - - + -
312A LEU* 5.4 0.2 - - - +
317A LEU* 3.9 5.5 - - - +
322A PHE* 4.5 1.6 - - - -
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 4.6 2.8 - - - +
64A ARG* 3.3 43.8 - - - +
67A HIS* 2.9 30.1 + - - +
68A THR 3.1 17.8 + - - -
70A GLY* 3.6 15.0 - - - +
71A THR 3.3 9.9 - - - +
101A LEU* 1.3 80.0 - - - +
103A HIS* 1.3 64.0 + - - +
104A ALA* 3.4 13.0 - - - +
118A SER* 4.0 3.1 + - - +
119A PHE* 3.8 3.1 + - - -
120A SER* 2.9 33.4 + - - +
317A LEU* 3.9 26.5 - - + +
318A GLU* 4.6 1.0 + - - +
322A PHE* 3.7 16.8 - - + -
999A HEM 2.8 40.8 + - - +
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Residues in contact with HIS 103 (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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70A GLY* 3.0 3.8 - - - -
71A THR* 2.7 38.5 + - + +
101A LEU* 3.5 16.1 - - + +
102A ARG* 1.3 72.1 - - - +
104A ALA* 1.3 61.9 + - - +
118A SER 2.8 25.8 - - - -
119A PHE* 3.7 16.1 - - - -
187A PHE* 3.5 38.2 + + + +
192A TYR* 3.3 27.7 + + - -
258A TYR* 3.6 15.8 - + - -
269A TYR* 2.7 36.1 - + - -
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Residues in contact with ALA 104 (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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67A HIS* 3.8 11.7 - - + +
69A VAL 3.1 17.7 - - - +
70A GLY* 3.9 1.8 - - - -
102A ARG* 3.4 25.1 - - - +
103A HIS* 1.3 76.3 - - - +
105A ASN* 1.3 65.9 + - - +
117A ARG* 3.4 5.4 - - - -
118A SER* 2.9 41.3 + - - +
187A PHE* 3.7 8.3 - - - -
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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