Contacts of the helix formed by residues 119 - 131 (chain A) in PDB entry 3UZU
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 PRO 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 4.9 17.5 - - + -
117A ASN* 3.8 7.4 - - - +
118A LEU* 1.3 85.8 - - + +
120A TYR* 1.3 60.3 - - - +
121A ASN* 3.4 18.3 + - - +
122A ILE* 3.6 14.1 + - + -
123A SER* 2.7 29.3 + - - -
145A GLN* 5.4 2.7 - - + +
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Residues in contact with TYR 120 (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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14A LYS* 5.7 9.9 - - - +
119A PRO* 1.3 73.1 - - - +
121A ASN* 1.3 69.9 + - - +
123A SER* 3.1 21.2 + - - -
124A SER 4.5 1.4 + - - -
145A GLN* 3.6 39.6 - - - +
147A GLU* 5.3 6.1 - - + -
148A VAL* 3.7 26.9 - - + -
151A ARG* 3.8 29.3 + - - -
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Residues in contact with ASN 121 (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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119A PRO* 3.7 16.3 - - - +
120A TYR* 1.3 87.1 - - + +
122A ILE* 1.3 91.7 + - - +
125A PRO* 3.5 17.7 - - - +
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Residues in contact with ILE 122 (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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94A ASP* 5.0 7.4 - - - +
96A LEU* 3.6 37.2 - - + +
118A LEU* 4.2 9.6 - - + -
119A PRO* 3.8 30.5 - - + +
121A ASN* 1.3 98.9 + - - +
123A SER* 1.3 60.8 + - - +
124A SER 3.5 0.7 - - - -
125A PRO* 3.4 7.9 - - + +
126A LEU* 2.9 48.3 + - + +
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Residues in contact with SER 123 (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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118A LEU* 3.7 15.3 + - - +
119A PRO 2.7 23.0 + - - -
120A TYR* 3.1 13.4 + - - -
121A ASN 3.3 0.2 - - - -
122A ILE* 1.3 78.6 - - - +
124A SER* 1.3 60.0 + - - +
126A LEU* 3.9 0.9 - - - +
127A LEU* 2.9 38.3 + - - +
144A LEU* 3.8 14.9 - - - +
145A GLN 5.6 0.3 + - - -
148A VAL* 3.9 28.3 - - - +
151A ARG* 6.3 0.2 - - - -
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Residues in contact with SER 124 (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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120A TYR 4.5 1.8 + - - -
123A SER* 1.3 79.4 - - - +
125A PRO* 1.3 72.3 - - - +
127A LEU* 3.3 2.8 + - - +
128A PHE* 2.9 41.7 + - - -
148A VAL* 5.5 0.5 - - - +
151A ARG* 4.3 12.6 + - - -
164A LEU* 3.7 28.7 - - - +
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Residues in contact with PRO 125 (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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96A LEU* 3.4 26.8 - - + +
121A ASN 3.5 21.1 - - - +
122A ILE* 3.4 14.1 - - + +
124A SER* 1.3 97.0 - - - +
126A LEU* 1.3 56.5 + - - +
128A PHE* 3.5 7.6 + - + +
129A HIS* 2.9 28.1 + - - +
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Residues in contact with LEU 126 (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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45A ILE* 4.0 20.0 - - + -
95A ALA* 3.8 34.5 - - + +
96A LEU* 3.9 8.4 - - - +
100A PHE* 4.6 3.1 - - + -
118A LEU* 3.7 34.8 - - + -
122A ILE* 2.9 32.1 + - + +
123A SER 4.0 2.5 - - - +
125A PRO* 1.3 74.2 - - - +
127A LEU* 1.3 67.3 + - - +
129A HIS* 3.1 14.4 + - + +
130A LEU* 2.9 39.4 + - + +
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Residues in contact with LEU 127 (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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118A LEU* 4.9 6.5 - - + -
123A SER* 2.9 26.4 + - - +
124A SER 3.9 2.9 - - - +
126A LEU* 1.3 77.6 - - - +
128A PHE* 1.3 60.2 + - - +
130A LEU* 3.5 6.9 + - + +
131A MET* 3.5 22.5 + - - +
140A GLN* 4.6 2.2 - - - +
142A PHE* 3.8 23.8 - - + -
144A LEU* 4.5 8.3 - - + -
148A VAL* 4.5 2.9 - - + -
152A MET* 3.9 26.2 - - + -
164A LEU* 4.4 20.6 - - + -
168A LEU* 4.3 15.6 - - + +
172A TYR* 4.8 1.4 + - - -
198A MET* 3.7 34.7 - - + +
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Residues in contact with PHE 128 (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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124A SER* 2.9 35.2 + - - +
125A PRO* 3.9 6.3 - - + +
127A LEU* 1.3 74.6 - - - +
129A HIS* 1.3 64.8 + - - +
131A MET* 3.2 33.9 + - - +
132A SER 4.4 1.0 + - - -
163A ARG* 3.9 28.5 - - + -
164A LEU* 3.9 35.2 - - + -
167A MET* 4.0 26.7 - - + -
168A LEU* 5.5 0.7 - - + -
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Residues in contact with HIS 129 (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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95A ALA 3.5 14.3 + - - -
96A LEU* 3.3 35.3 + - + -
97A THR* 4.8 2.5 - - - -
98A PHE 2.9 29.1 + - - -
99A ASP* 5.6 0.2 - - - -
100A PHE* 4.2 4.7 - + - -
125A PRO 2.9 21.2 + - - +
126A LEU* 3.1 12.8 + - + +
128A PHE* 1.3 73.3 - - - +
130A LEU* 1.3 61.8 + - - +
131A MET 3.3 1.0 + - - -
132A SER* 3.5 11.2 + - - -
133A PHE* 3.5 33.2 - + - -
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Residues in contact with LEU 130 (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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45A ILE* 4.5 2.0 - - + -
100A PHE* 3.6 40.6 - - + -
114A ILE* 3.8 21.3 - - + -
126A LEU* 2.9 33.2 + - + +
127A LEU* 3.9 7.2 - - - +
128A PHE 3.2 0.4 - - - -
129A HIS* 1.3 74.9 - - + +
131A MET* 1.3 65.6 + - - +
132A SER 3.2 0.2 - - - -
133A PHE* 3.0 21.5 + - + +
134A ALA* 3.4 7.3 + - - -
140A GLN* 3.8 26.2 + - - +
142A PHE* 3.6 32.3 - - + -
172A TYR* 3.8 5.1 + - - +
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Residues in contact with MET 131 (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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127A LEU 3.5 14.3 + - - +
128A PHE* 3.2 33.7 + - - +
130A LEU* 1.3 77.6 - - - +
132A SER* 1.3 60.6 + - - +
134A ALA* 3.1 19.1 + - - +
135A PRO* 4.5 1.6 - - - +
167A MET* 3.6 38.6 - - + +
168A LEU* 4.1 11.4 - - + -
170A TYR* 4.8 6.7 - - + -
171A ARG* 3.7 26.8 + - + -
172A TYR* 3.5 19.5 - - + +
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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