Contacts of the helix formed by residues 84 - 96 (chain A) in PDB entry 1UU1
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY* 2.6 20.2 + - - -
83A ASN* 1.3 77.3 - - - +
85A ALA* 1.3 66.0 + - - +
86A ASP 3.0 2.2 + - - -
87A GLU 3.3 5.0 + - - -
88A ILE* 3.8 4.0 + - - +
210A ARG* 3.4 23.8 + - - -
211A VAL 3.9 0.4 - - - -
212A GLY 3.7 10.5 + - - -
1335A PMP 3.7 14.4 - - - -
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Residues in contact with ALA 85 (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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84A GLY* 1.3 71.7 - - - -
86A ASP* 1.3 63.2 + - - +
88A ILE* 3.0 21.5 + - - +
89A ILE* 3.1 16.8 + - + +
173A ASP* 5.5 1.1 - - - +
175A ALA* 5.6 0.9 - - + -
197A ILE* 3.9 18.5 - - + +
198A ARG 4.0 2.7 - - - +
199A THR* 3.9 13.2 - - + -
212A GLY* 3.8 8.9 - - - -
1335A PMP 2.7 40.6 + - + +
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Residues in contact with ASP 86 (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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83A ASN 4.7 0.7 - - - +
85A ALA* 1.3 78.4 - - - +
87A GLU* 1.3 56.9 + - - +
89A ILE* 3.0 7.9 + - - +
90A TYR* 2.9 28.1 + - - +
106A TYR* 2.7 30.2 + - - -
112A PHE* 3.5 23.3 - - + -
210A ARG* 3.7 13.4 + - - +
1335A PMP 3.0 24.6 + - - +
1336A HSA 2.9 21.0 + - - -
229B LEU* 3.7 15.0 - - + -
230B PRO* 4.6 4.0 - - - +
231B PHE* 4.5 4.5 + - - -
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Residues in contact with GLU 87 (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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82A GLY* 3.3 3.5 - - - -
83A ASN* 2.7 45.3 + - - +
84A GLY 3.3 2.2 + - - -
85A ALA 3.2 0.8 - - - -
86A ASP* 1.3 79.1 - - - +
88A ILE* 1.3 58.6 + - - +
90A TYR* 3.5 3.0 - - + +
91A VAL* 2.9 46.7 + - + +
224A TYR* 4.3 2.5 + - - -
228A ARG* 5.2 2.5 - - - -
229A LEU* 3.9 21.5 + - - +
232A ASN* 2.7 44.5 - - - +
83B ASN* 4.5 1.0 + - - -
87B GLU* 5.2 0.5 - - - +
229B LEU* 3.8 23.8 - - + +
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Residues in contact with ILE 88 (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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82A GLY* 3.7 11.0 - - - +
84A GLY 3.9 3.6 - - - +
85A ALA* 3.0 6.2 + - - +
87A GLU* 1.3 76.5 - - - +
89A ILE* 1.3 60.5 + - - +
91A VAL* 3.1 11.3 - - - +
92A MET* 2.9 37.3 - - - +
197A ILE* 3.9 29.4 - - + -
212A GLY* 3.5 10.1 - - - -
213A TYR* 3.3 32.8 - - - +
214A VAL* 3.2 38.6 - - + -
224A TYR* 3.7 18.4 - - + +
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Residues in contact with ILE 89 (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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85A ALA* 3.1 15.9 + - + +
86A ASP* 3.0 8.4 + - - +
88A ILE* 1.3 78.9 - - - +
90A TYR* 1.3 63.0 + - - +
92A MET* 3.3 3.5 + - - +
93A MET* 3.1 47.4 + - + +
106A TYR* 3.9 9.4 - - + -
109A TYR* 3.9 19.5 - - + -
112A PHE* 3.9 13.5 - - + -
143A PHE* 3.8 15.6 - - + -
173A ASP* 3.5 23.1 - - - +
197A ILE* 4.2 16.2 - - + -
1335A PMP 3.9 17.0 - - + -
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Residues in contact with TYR 90 (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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86A ASP 2.9 16.0 + - - +
87A GLU* 3.5 11.0 - - + +
89A ILE* 1.3 77.7 - - - +
91A VAL* 1.3 69.1 + - + +
93A MET* 3.4 14.3 + - - +
94A LEU* 3.5 13.7 + - + +
112A PHE* 4.0 30.7 - + + -
115A ALA* 4.9 5.4 - - + -
116A VAL* 3.6 25.9 - - + +
90B TYR* 4.7 10.1 - + - -
91B VAL* 3.9 14.2 - - + +
94B LEU* 3.6 22.5 - - + +
227B VAL* 2.5 31.9 + - - +
228B ARG* 4.0 1.1 - - - -
229B LEU* 3.8 35.7 - - + -
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Residues in contact with VAL 91 (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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87A GLU* 2.9 34.7 + - + +
88A ILE* 3.1 6.3 - - - +
90A TYR* 1.3 75.5 - - + +
92A MET* 1.3 60.7 + - - +
94A LEU* 2.7 32.3 + - - +
95A MET* 3.1 14.4 + - - +
224A TYR* 3.0 38.1 - - + +
227A VAL* 4.3 8.0 - - + +
228A ARG* 4.0 27.8 - - + +
229A LEU 5.3 0.2 - - - +
90B TYR* 4.1 12.8 - - + +
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Residues in contact with MET 92 (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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88A ILE* 2.9 31.1 + - + +
89A ILE 3.3 4.9 + - - +
91A VAL* 1.3 78.8 - - + +
93A MET* 1.3 58.7 + - - +
95A MET* 2.8 26.2 + - - -
96A PHE* 3.2 27.3 + - + -
141A VAL* 4.5 1.6 - - + -
143A PHE* 3.8 14.4 - - + -
169A PHE* 3.7 24.7 - - + -
171A ALA* 4.1 14.4 - - + -
195A ALA* 4.1 8.3 - - + -
197A ILE* 3.9 25.1 - - - -
214A VAL* 5.1 0.4 - - - -
220A PHE* 3.4 36.1 - - + -
224A TYR* 4.9 0.2 - - + -
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Residues in contact with MET 93 (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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89A ILE* 3.1 21.9 + - + +
90A TYR 3.6 9.0 - - - +
91A VAL 3.1 0.4 - - - -
92A MET* 1.3 77.1 - - - +
94A LEU* 1.3 60.2 + - - +
95A MET 3.3 0.2 - - - -
96A PHE 4.0 10.9 - - - +
99A SER* 3.4 20.1 + - - +
101A PHE* 4.0 10.5 - - + -
109A TYR* 3.4 30.7 - - + +
112A PHE* 3.9 10.3 - - + -
113A ALA* 3.5 33.0 - - - -
116A VAL* 4.0 11.4 - - + -
118A ALA* 3.3 21.5 - - + +
141A VAL* 5.3 0.4 - - - -
143A PHE* 3.6 28.3 - - + -
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Residues in contact with LEU 94 (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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90A TYR* 3.8 8.7 - - + +
91A VAL* 2.7 17.1 + - - +
93A MET* 1.3 74.3 - - - +
95A MET* 1.3 59.6 + - - +
96A PHE 3.6 2.3 + - - +
116A VAL* 3.2 45.8 - - + +
227A VAL* 4.2 9.2 - - + -
10B ARG* 3.7 19.1 + - - -
90B TYR* 3.4 33.7 - - + +
94B LEU* 3.8 15.9 - - + -
116B VAL* 3.9 28.5 - - + +
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Residues in contact with MET 95 (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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91A VAL 3.5 9.0 - - - +
92A MET* 2.8 21.9 + - - +
94A LEU* 1.3 79.5 - - - +
96A PHE* 1.3 69.9 + - + -
220A PHE* 3.6 29.2 - - + -
223A ALA* 3.4 20.0 - - + -
224A TYR* 3.1 49.6 - - - +
227A VAL* 3.9 21.5 - - + -
4B LEU* 6.0 1.6 - - + -
7B ILE* 3.3 40.5 - - + +
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Residues in contact with PHE 96 (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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92A MET* 3.2 29.8 + - + +
93A MET 4.0 12.3 + - - +
94A LEU 4.6 2.1 - - - +
95A MET* 1.3 89.7 - - + +
97A ASP* 1.3 66.3 + - - +
98A ARG* 3.4 1.7 - - - +
99A SER* 5.4 0.6 + - - +
118A ALA* 5.6 1.9 - - - +
139A GLY* 3.3 19.7 - - - +
140A ASP 3.8 9.0 - - - -
141A VAL* 3.4 37.0 - - + -
169A PHE* 3.5 40.8 - + + -
220A PHE* 3.9 25.6 - + - -
4B LEU* 4.1 26.5 - - + -
7B ILE* 6.1 0.2 - - - -
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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