Contacts of the helix formed by residues 107 - 119 (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 GLY 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A VAL 2.9 7.6 + - - -
104A LEU 3.4 5.1 + - - -
105A ALA 3.3 3.2 + - - -
106A TRP* 1.3 78.0 - - - +
108A PRO* 1.3 70.8 - - - +
109A GLU 3.4 2.7 - - - -
110A ARG* 3.1 5.0 + - - -
111A PHE* 2.8 27.5 + - - +
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Residues in contact with PRO 108 (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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103A VAL* 3.3 30.2 - - + +
104A LEU* 4.4 20.0 - - + +
107A GLY* 1.3 80.7 - - - +
109A GLU* 1.3 64.0 + - - +
112A PHE* 2.9 40.6 + - + -
136A LEU* 4.8 12.6 - - + -
139A LEU* 3.6 18.4 - - + -
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Residues in contact with GLU 109 (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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107A GLY 3.4 0.8 - - - -
108A PRO* 1.3 78.1 - - - +
110A ARG* 1.3 58.9 + - - +
113A GLY* 3.0 25.8 + - - -
139A LEU* 3.6 30.0 - - + +
143A ILE* 3.8 10.8 - - + +
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Residues in contact with ARG 110 (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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105A ALA 4.5 3.8 + - - -
106A TRP* 2.8 59.2 + - + +
107A GLY* 3.1 8.0 + - - +
109A GLU* 1.3 78.0 - - - +
111A PHE* 1.3 60.3 + - - +
113A GLY* 3.3 1.0 + - - -
114A LEU* 2.8 53.1 + - + +
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Residues in contact with PHE 111 (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* 3.8 26.0 - - + -
76A VAL* 4.3 8.5 - - + -
96A LEU* 3.9 9.2 - - + -
98A THR* 4.0 11.0 - - + -
102A PRO 4.0 9.4 - - - -
103A VAL* 3.7 48.7 - - + -
106A TRP* 4.1 19.0 - + + +
107A GLY 2.8 20.4 + - - +
108A PRO 3.8 2.7 - - - +
110A ARG* 1.3 74.6 - - - +
112A PHE* 1.3 79.5 + + - +
114A LEU* 3.3 5.6 + - - +
115A PHE* 3.1 63.7 + + + -
123A VAL* 5.2 1.6 - - + -
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Residues in contact with PHE 112 (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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100A LEU* 5.7 0.4 - - + -
103A VAL* 4.0 11.2 - - + -
108A PRO* 2.9 39.8 + - + +
111A PHE* 1.3 91.8 - + - +
113A GLY* 1.3 63.1 + - - +
115A PHE* 3.4 1.7 + - - +
116A LYS* 2.9 26.7 + - - +
123A VAL* 4.2 22.9 - - + -
125A LEU* 4.5 15.0 - - + -
136A LEU* 3.7 34.3 - - + -
139A LEU* 4.5 5.2 - - + -
140A ALA* 3.8 26.0 - - + -
143A ILE* 3.6 16.2 - - + -
145A LEU* 3.6 25.0 - - + +
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Residues in contact with GLY 113 (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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109A GLU 3.0 20.5 + - - -
110A ARG* 3.7 1.1 - - - -
112A PHE* 1.3 77.5 - - - +
114A LEU* 1.3 55.9 + - - +
116A LYS* 3.4 1.9 + - - +
117A GLN* 2.9 37.4 + - - +
143A ILE* 3.9 15.2 - - - +
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Residues in contact with LEU 114 (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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76A VAL* 5.8 0.9 - - + -
77A GLN* 5.2 2.2 - - - +
80A LEU* 3.6 29.2 - - + +
84A ARG* 5.1 9.3 + - - +
106A TRP* 3.9 24.7 - - + -
110A ARG* 2.8 40.0 + - + +
111A PHE* 3.7 5.2 - - - +
113A GLY* 1.3 77.7 - - - +
115A PHE* 1.3 58.5 + - + +
117A GLN* 3.4 19.8 + - - +
118A ALA* 2.9 28.1 + - - +
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Residues in contact with PHE 115 (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* 4.8 3.6 - - + -
76A VAL* 4.0 19.1 - - + -
79A ALA* 4.2 9.0 - - + -
80A LEU* 3.6 35.0 - - + -
83A VAL* 4.0 22.9 - - + -
96A LEU* 3.5 36.1 - - + -
111A PHE* 3.1 63.8 + + + +
112A PHE* 4.1 4.5 - - - +
114A LEU* 1.3 74.7 - - + +
116A LYS* 1.3 65.1 + - - +
118A ALA* 3.3 7.6 + - - +
119A GLY 3.3 0.7 + - - -
120A ALA* 3.0 31.7 + - + +
123A VAL* 5.5 2.9 - - + -
145A LEU* 5.3 4.5 - - + -
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Residues in contact with LYS 116 (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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112A PHE 2.9 18.8 + - - +
113A GLY 3.7 3.6 - - - +
115A PHE* 1.3 77.3 - - - +
117A GLN* 1.3 63.0 + - - +
119A GLY* 3.1 14.7 + - - -
120A ALA 3.8 16.3 + - - +
121A THR* 4.8 4.0 + - - +
143A ILE* 3.5 24.5 - - + +
144A GLY* 2.8 37.7 + - - +
145A LEU* 3.8 15.4 - - + +
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Residues in contact with GLN 117 (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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84A ARG* 5.4 2.4 + - - +
113A GLY 2.9 21.0 + - - +
114A LEU* 3.4 21.2 - - - +
116A LYS* 1.3 79.7 - - + +
118A ALA* 1.3 59.8 + - - +
119A GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 118 (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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80A LEU* 3.8 20.6 - - + +
83A VAL* 3.8 12.7 - - + +
84A ARG* 3.6 53.4 - - + +
87A ARG* 4.1 4.2 - - - +
114A LEU 2.9 17.4 + - - +
115A PHE* 3.6 7.2 - - - +
116A LYS 3.2 0.6 - - - -
117A GLN* 1.3 76.6 - - - +
119A GLY* 1.3 56.5 + - - +
120A ALA 3.8 0.4 - - - -
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Residues in contact with GLY 119 (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* 4.2 4.9 - - - -
87A ARG* 2.9 46.7 + - - -
94A LEU* 4.3 0.9 - - - +
116A LYS 3.1 10.3 + - - -
117A GLN 3.1 2.5 - - - -
118A ALA* 1.3 79.6 - - - +
120A ALA* 1.3 63.6 + - - +
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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