Contacts of the strand formed by residues 70 - 79 (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 GLY 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 4.7 2.8 - - - +
68A THR 4.1 0.2 + - - -
69A VAL* 1.3 77.4 - - - +
71A THR* 1.3 63.6 + - - -
102A ARG* 3.6 10.2 - - - +
103A HIS 3.0 13.7 - - - -
104A ALA* 3.9 4.0 - - - -
255A ARG* 3.5 21.0 - - - +
317A LEU* 4.2 8.9 - - - +
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Residues in contact with THR 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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70A GLY* 1.3 76.1 - - - -
72A GLY* 1.3 62.8 + - - +
102A ARG* 3.3 5.7 - - - +
103A HIS* 2.7 37.0 + - + +
187A PHE* 3.9 25.4 - - + -
255A ARG* 3.6 23.1 + - - -
258A TYR* 3.8 29.4 - - + -
259A VAL* 3.8 16.2 - - - +
317A LEU* 3.5 14.5 - - - +
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Residues in contact with GLY 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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71A THR* 1.3 86.9 + - - +
73A GLY* 1.3 58.5 + - - -
101A LEU* 3.2 16.4 - - - -
102A ARG* 4.4 0.2 - - - -
258A TYR* 4.0 20.4 - - - -
259A VAL* 5.7 1.9 - - - +
262A LEU* 3.7 15.2 - - - +
311A PRO* 4.0 1.9 - - - +
312A LEU* 4.0 11.6 + - - -
317A LEU* 3.8 6.5 - - - +
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Residues in contact with GLY 73 (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* 1.3 74.0 - - - -
74A ILE* 1.3 66.3 + - - +
100A ARG* 3.5 3.1 - - - +
101A LEU* 3.0 31.2 + - - +
262A LEU* 4.5 0.2 - - - -
308A ILE* 3.7 15.0 - - - +
310A THR 3.1 13.5 - - - -
312A LEU* 3.9 16.3 - - - +
317A LEU* 4.8 1.0 - - - +
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Residues in contact with ILE 74 (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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73A GLY* 1.3 77.3 - - - +
75A GLY* 1.3 60.5 + - - +
99A ALA 3.1 7.9 - - - +
100A ARG* 3.8 9.6 - - + -
125A ASP* 3.6 33.7 - - - +
308A ILE* 4.1 1.8 - - - -
309A LYS* 3.0 19.9 + - - +
310A THR* 2.8 42.6 + - + +
311A PRO 5.5 0.4 - - - +
312A LEU* 3.2 33.0 - - + -
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Residues in contact with GLY 75 (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* 1.3 76.5 - - - +
76A GLU* 1.3 61.5 + - - +
98A PRO* 3.8 4.0 - - - +
99A ALA* 2.9 30.2 + - - -
307A SER 3.0 15.3 - - - -
308A ILE* 3.9 7.7 - - - +
309A LYS* 3.9 9.6 - - - -
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Residues in contact with GLU 76 (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* 1.3 74.7 - - - +
77A ILE* 1.3 69.7 + - - +
78A THR* 4.1 14.0 + - - +
96A THR* 3.4 27.5 + - - +
97A PHE 3.4 13.6 - - - +
98A PRO* 5.1 1.6 - - + -
99A ALA* 4.5 0.4 - - - +
305A LYS 3.7 2.6 - - - +
306A VAL* 3.7 1.1 - - - -
307A SER* 2.8 36.7 + - - -
308A ILE* 5.2 0.8 - - - +
309A LYS* 3.5 27.4 + - - +
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Residues in contact with ILE 77 (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* 1.3 74.1 - - - +
78A THR* 1.3 64.1 + - - +
79A ILE* 4.5 1.1 - - + -
95A ARG 3.7 0.9 - - - +
96A THR* 3.0 4.9 - - - -
97A PHE* 2.8 45.9 + - + +
99A ALA* 3.6 27.6 - - + -
121A ILE* 4.2 15.0 - - + -
122A LYS 4.2 2.2 - - - +
123A PHE* 3.8 54.3 - - + -
271A LEU* 5.1 0.9 - - + -
304A ALA* 3.9 20.2 - - + -
305A LYS 3.4 4.7 - - - +
306A VAL* 4.4 18.6 - - + -
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Residues in contact with THR 78 (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* 4.1 13.0 + - - +
77A ILE* 1.3 76.2 - - - +
79A ILE* 1.3 74.6 + - - +
80A VAL* 4.4 0.7 - - - -
81A ASN* 5.8 3.8 - - - +
94A GLY* 3.8 7.9 - - - +
95A ARG 3.3 3.1 - - - +
96A THR* 3.6 27.1 - - + +
304A ALA* 3.6 3.1 - - - -
305A LYS* 2.8 47.5 + - - +
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Residues in contact with ILE 79 (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* 4.5 4.7 - - + -
78A THR* 1.3 77.1 - - - +
80A VAL* 1.3 76.5 + - + +
81A ASN* 3.6 1.0 + - - +
83A PRO* 5.4 0.2 - - + -
85A PHE* 4.4 10.1 - - + -
91A PHE* 3.8 44.2 - - + +
92A THR 3.2 28.5 - - - +
93A ALA* 4.1 0.9 - - - -
94A GLY* 3.0 17.4 + - - +
95A ARG* 2.8 19.6 + - + +
97A PHE* 4.0 21.3 - - + -
123A PHE* 4.7 1.8 - - + -
303A LEU* 3.4 13.0 - - + +
304A ALA* 3.5 16.6 - - + -
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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