Contacts of the helix formed by residues 75 - 90 (chain A) in PDB entry 1UJP
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 SER 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.5 6.3 - - - -
70A LEU* 5.8 0.7 - - - -
73A GLY 3.5 6.9 + - - -
74A MET* 1.3 80.3 - - - +
76A VAL* 1.3 59.4 + - - +
77A GLN* 3.5 8.7 + - - +
78A GLY* 3.1 17.6 + - - +
79A ALA* 2.8 29.1 + - - +
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Residues in contact with VAL 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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50A LEU* 4.1 27.6 - - + +
75A SER* 1.3 74.2 - - - +
77A GLN* 1.3 58.3 + - - +
79A ALA* 3.2 2.9 + - - +
80A LEU* 2.9 36.4 + - + +
102A PRO* 4.5 8.3 - - + -
106A TRP* 3.4 50.0 - - + +
111A PHE* 4.3 7.2 - - + -
114A LEU* 5.8 1.1 - - + -
115A PHE* 4.0 21.9 - - + -
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Residues in contact with GLN 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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75A SER* 3.2 8.8 + - - +
76A VAL* 1.3 78.6 - - - +
78A GLY* 1.3 63.4 + - - +
80A LEU* 3.3 20.2 + - - +
81A GLU* 3.3 21.3 + - - +
84A ARG* 5.0 7.3 + - - +
106A TRP* 3.6 31.6 - - + -
114A LEU* 5.2 1.7 - - - +
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Residues in contact with GLY 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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29A ARG* 5.2 4.9 + - - -
74A MET* 3.7 15.2 - - - +
75A SER* 3.1 19.3 + - - -
77A GLN* 1.3 76.7 - - - +
79A ALA* 1.3 61.4 + - - +
81A GLU* 3.6 5.2 + - - +
82A LEU* 3.2 26.5 + - - +
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Residues in contact with ALA 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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24A ALA* 4.5 10.8 - - + -
48A ILE* 5.9 0.8 - - + +
50A LEU* 3.6 24.2 - - + -
74A MET* 3.6 10.3 - - - -
75A SER 2.8 16.7 + - - +
76A VAL 3.6 3.6 - - - +
78A GLY* 1.3 73.0 - - - +
80A LEU* 1.3 61.0 + - - +
82A LEU* 3.2 8.5 + - - +
83A VAL* 2.9 33.0 + - + +
96A LEU* 5.1 4.9 - - + -
115A PHE* 4.2 11.4 - - + -
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Residues in contact with LEU 80 (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 VAL* 2.9 29.8 + - + +
77A GLN* 3.3 24.9 + - - +
79A ALA* 1.3 77.6 - - - +
81A GLU* 1.3 62.0 + - - +
83A VAL* 3.3 4.8 + - - +
84A ARG* 3.1 44.3 + - - +
106A TRP* 5.4 0.4 - - + -
114A LEU* 3.6 52.0 - - + +
115A PHE* 3.6 37.0 - - + -
118A ALA* 3.8 6.0 - - + +
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Residues in contact with GLU 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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29A ARG* 3.5 22.2 - - - +
77A GLN 3.3 9.6 + - - +
78A GLY* 4.0 7.9 - - - +
80A LEU* 1.3 79.3 - - - +
82A LEU* 1.3 59.0 + - - +
84A ARG* 3.1 33.2 + - - +
85A GLU* 2.9 45.1 + - - +
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Residues in contact with LEU 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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24A ALA* 4.0 8.7 - - + -
25A GLY* 3.9 9.0 - - - +
29A ARG* 3.9 34.3 - - + +
32A PHE* 3.8 28.0 - - + -
33A LEU* 3.9 27.6 - - + -
48A ILE* 5.4 1.8 - - + -
74A MET* 3.5 31.6 - - + -
78A GLY 3.2 14.5 + - - +
79A ALA* 3.2 7.8 + - - +
81A GLU* 1.3 74.6 - - - +
83A VAL* 1.3 60.3 + - + +
85A GLU* 3.2 3.5 + - - +
86A VAL* 2.9 35.8 + - - +
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Residues in contact with VAL 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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48A ILE* 4.4 19.5 - - + -
79A ALA* 2.9 18.8 + - - +
80A LEU 3.3 7.8 + - - +
82A LEU* 1.3 76.7 - - - +
84A ARG* 1.3 57.9 + - - +
86A VAL* 3.3 5.8 + - - +
87A ARG* 2.9 27.5 + - - +
94A LEU* 4.4 7.7 - - + +
96A LEU* 4.5 11.9 - - + -
115A PHE* 4.0 20.6 - - + +
118A ALA* 3.8 21.8 - - + +
119A GLY 4.2 2.7 - - - -
120A ALA* 3.9 27.1 - - + +
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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 GLN* 5.0 6.9 + - - +
80A LEU* 3.1 39.8 + - - +
81A GLU* 3.1 52.7 + - - +
83A VAL* 1.3 77.5 - - - +
85A GLU* 1.3 56.3 + - + +
87A ARG* 3.3 3.0 + - - +
88A ALA* 3.0 27.7 + - - +
114A LEU* 5.1 9.9 + - - +
117A GLN* 5.4 2.2 + - - +
118A ALA* 3.6 32.3 - - + +
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Residues in contact with GLU 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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29A ARG* 2.6 34.5 + - - -
33A LEU* 3.3 32.7 - - + +
81A GLU* 2.9 34.1 + - - +
82A LEU* 3.2 5.6 + - - +
84A ARG* 1.3 78.0 - - + +
86A VAL* 1.3 62.3 + - - +
88A ALA* 3.3 14.1 + - - +
89A LEU* 3.3 22.4 + - + +
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Residues in contact with VAL 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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32A PHE* 4.0 18.4 - - + -
33A LEU* 4.7 5.4 - - + -
36A VAL* 4.1 20.9 - - + -
46A LEU* 3.8 15.3 - - + -
48A ILE* 4.0 19.5 - - + -
82A LEU 2.9 20.9 + - - +
83A VAL 3.8 3.6 - - - +
85A GLU* 1.3 76.4 - - - +
87A ARG* 1.3 58.8 + - - +
89A LEU* 2.9 23.7 + - - +
90A THR* 3.1 16.2 + - + +
94A LEU* 3.8 28.9 - - + -
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Residues in contact with ARG 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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83A VAL 2.9 17.9 + - - +
84A ARG 3.3 5.1 + - - +
86A VAL* 1.3 76.8 - - - +
88A ALA* 1.3 60.8 + - - +
90A THR 2.9 39.0 + - - +
91A GLU* 3.4 12.7 + - - +
92A LYS 2.8 26.4 + - - -
93A PRO* 4.5 0.2 - - - +
94A LEU* 3.4 24.8 - - + +
118A ALA 4.1 9.2 - - - +
119A GLY* 2.9 37.5 + - - -
121A THR* 3.1 23.4 + - - -
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Residues in contact with ALA 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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84A ARG 3.0 13.5 + - - +
85A GLU* 3.6 13.2 - - - +
86A VAL 3.1 0.4 - - - -
87A ARG* 1.3 77.5 - - - +
89A LEU* 1.3 63.2 + - + +
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Residues in contact with LEU 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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33A LEU* 5.1 13.9 - - + +
36A VAL* 4.1 24.7 - - + -
37A GLU* 5.3 5.8 - - + +
40A LEU* 4.2 17.4 - - + +
85A GLU 3.3 17.0 - - - +
86A VAL* 2.9 9.7 + - - +
88A ALA* 1.3 84.8 - - + +
90A THR* 1.3 59.0 + - - +
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Residues in contact with THR 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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40A LEU* 4.0 26.2 - - + +
86A VAL* 3.1 15.2 + - + +
87A ARG* 2.9 33.3 + - - +
88A ALA 3.6 0.2 - - - -
89A LEU* 1.3 82.5 - - - +
91A GLU* 1.3 69.9 + - - +
92A LYS* 3.0 34.7 + - + +
94A LEU* 4.1 22.0 - - + -
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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