Contacts of the helix formed by residues 80 - 91 (chain A) in PDB entry 1UHG
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 HIS 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.4 21.3 - - + +
42A TYR* 4.5 1.1 - + - -
43A LEU* 3.3 26.6 - - + +
64A GLY 2.8 28.9 + - - -
65A PHE* 3.2 41.7 - + + -
70A GLU* 3.0 25.1 + - + -
78A ASN 3.3 0.2 + - - -
79A VAL* 1.3 80.8 - - + +
81A SER* 1.3 64.1 + - - +
82A SER 3.3 2.9 - - - -
83A LEU* 3.1 6.6 + - + +
84A ARG* 2.9 26.5 + - + +
124A LEU* 5.0 0.4 - - + +
125A TYR* 2.8 27.5 + - - +
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Residues in contact with SER 81 (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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63A PRO* 3.6 17.7 + - - +
64A GLY* 3.9 1.5 + - - -
77A VAL 4.4 4.9 - - - -
78A ASN* 3.1 25.9 + - - +
79A VAL 3.0 4.8 - - - -
80A HIS* 1.3 77.7 - - - +
82A SER* 1.3 59.9 + - - +
84A ARG* 4.5 4.0 - - - -
85A ASP* 2.8 54.2 + - - -
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Residues in contact with SER 82 (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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3A ILE* 3.8 24.4 - - - +
62A LEU* 3.8 11.8 - - - +
63A PRO* 2.8 41.2 + - - -
65A PHE* 3.6 13.3 - - - -
81A SER* 1.3 81.0 + - - +
83A LEU* 1.3 59.8 + - - +
85A ASP* 4.7 2.4 - - - +
86A ILE* 3.8 23.7 + - - +
373A THR* 5.8 0.2 - - - +
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Residues in contact with LEU 83 (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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3A ILE* 4.4 10.5 - - + -
32A ILE* 3.3 46.0 - - + +
35A MET* 3.7 15.9 - - + +
36A SER* 3.7 26.2 - - - +
39A ALA* 3.9 14.6 - - + -
59A PHE* 4.5 4.0 - - + -
62A LEU* 6.0 0.7 - - + -
65A PHE* 4.0 16.8 - - + -
80A HIS* 3.1 7.3 + - + +
82A SER* 1.3 78.5 + - - +
84A ARG* 1.3 66.8 + - + +
85A ASP 3.2 1.6 - - - -
86A ILE* 3.2 6.3 + - - +
87A LEU* 3.1 30.6 + - + +
125A TYR* 5.3 2.2 - - + +
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Residues in contact with ARG 84 (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 VAL* 4.7 19.2 + - - +
79A VAL 3.6 16.2 + - - -
80A HIS* 2.9 27.0 + - + +
81A SER* 4.4 3.1 - - - +
83A LEU* 1.3 78.4 - - + +
85A ASP* 1.3 55.4 + - - +
87A LEU* 4.5 7.0 - - - +
88A ASN* 2.7 79.7 + - - +
123A GLU* 4.0 8.5 + - - -
124A LEU* 2.4 61.6 + - - +
125A TYR* 4.3 13.5 - - + +
126A ARG* 5.8 0.6 - - - +
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 5.0 8.3 - - - +
81A SER* 2.8 46.5 + - - +
82A SER* 4.7 3.1 - - - +
84A ARG* 1.3 78.3 + - - +
86A ILE* 1.3 58.6 + - + +
88A ASN* 4.0 9.7 + - - +
89A GLN* 3.1 28.9 + - - +
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Residues in contact with ILE 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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3A ILE* 3.8 26.7 - - + -
32A ILE* 4.5 12.6 - - + -
82A SER 3.8 7.9 - - - +
83A LEU 3.2 7.4 + - - +
85A ASP* 1.3 75.1 - - + +
87A LEU* 1.3 61.8 + - - +
89A GLN* 3.3 7.4 + - - +
90A ILE* 2.9 34.0 + - + +
370A HIS* 4.4 19.1 - - + +
373A THR* 3.6 33.0 - - + +
375A ALA* 3.7 16.8 - - + -
377A LEU* 4.2 24.5 - - + -
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Residues in contact with LEU 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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32A ILE* 4.2 18.2 - - + +
33A ALA* 5.0 2.0 - - - -
36A SER* 3.2 38.4 - - - +
83A LEU* 3.1 28.0 + - + +
84A ARG* 4.0 6.1 - - - +
86A ILE* 1.3 75.3 - - - +
88A ASN* 1.3 61.2 + - - +
90A ILE* 4.0 6.1 - - + -
91A THR* 2.7 41.9 + - + +
99A PHE* 4.0 23.3 - - + -
101A LEU* 3.6 26.5 - - + -
126A ARG* 5.2 1.6 - - - +
401A SO4 4.8 7.9 - - - +
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Residues in contact with ASN 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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77A VAL* 6.0 2.0 - - - +
84A ARG* 2.7 75.5 + - - +
85A ASP* 4.0 10.9 + - - +
87A LEU* 1.3 73.7 - - - +
89A GLN* 1.3 62.7 + - - +
91A THR* 3.3 11.0 + - - -
92A LYS* 3.3 30.9 - - - +
126A ARG* 3.8 20.8 + - - +
401A SO4 5.0 1.7 + - - -
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Residues in contact with GLN 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 ASP 3.1 19.6 + - - +
86A ILE* 3.7 6.5 + - - +
88A ASN* 1.3 77.9 - - - +
90A ILE* 1.3 65.2 + - + +
92A LYS* 3.3 29.4 + - + +
94A ASN* 5.7 0.2 + - - -
97A TYR* 4.0 9.6 + - - +
238A THR* 4.2 20.3 - - - +
370A HIS* 2.8 40.3 + - - -
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Residues in contact with ILE 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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32A ILE* 4.9 0.7 - - + -
86A ILE* 2.9 26.1 + - + +
87A LEU* 3.7 13.2 - - + +
89A GLN* 1.3 76.8 - - + +
91A THR* 1.3 61.8 + - - +
92A LYS 3.3 2.0 + - - +
97A TYR* 3.4 22.0 - - - +
99A PHE* 3.3 62.8 + - + +
239A MET* 3.6 26.7 - - + -
370A HIS* 4.3 20.6 - - + -
377A LEU* 4.1 22.0 - - + -
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Residues in contact with THR 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 LEU* 2.7 27.6 + - + +
88A ASN 3.3 3.3 + - - -
90A ILE* 1.3 74.6 - - - +
92A LYS* 1.3 65.4 + - - +
93A PRO* 4.2 0.5 - - - +
99A PHE* 3.9 37.1 - - + +
101A LEU* 4.4 14.4 - - + +
126A ARG* 3.2 31.6 + - - +
401A SO4 4.6 2.5 - - - +
93B PRO* 3.3 30.5 - - + +
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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