Contacts of the helix formed by residues 118 - 135 (chain A) in PDB entry 5YUS
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 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A CYS* 2.9 19.0 + - - +
116A HIS* 3.2 2.8 + - - -
117A GLY* 1.3 74.8 - - - +
119A ALA* 1.3 57.0 + - - +
120A THR* 3.5 8.1 + - - -
121A LEU* 2.9 38.2 + - - +
122A ILE* 2.9 33.2 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 4.0 22.4 - - + +
5A ILE* 3.5 5.4 - - + +
109A VAL* 3.8 29.4 - - + -
117A GLY 3.3 5.5 + - - -
118A SER* 1.3 69.8 - - - +
120A THR* 1.3 60.1 + - - +
122A ILE* 4.3 1.6 - - - -
123A ALA* 3.0 30.7 + - - +
142A VAL* 3.6 26.4 - - + +
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Residues in contact with THR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.2 6.9 + - - -
119A ALA* 1.3 77.3 - - - +
121A LEU* 1.3 65.0 + - + +
123A ALA 3.3 1.2 + - - -
124A GLN* 3.0 25.0 + - + +
142A VAL* 4.6 1.9 - - - +
161A GLN* 3.2 28.9 + - - +
163A VAL* 3.3 34.0 - - + +
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Residues in contact with LEU 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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115A CYS* 3.7 26.2 - - + +
116A HIS* 5.6 4.0 - - + +
118A SER* 2.9 28.7 + - - +
120A THR* 1.3 80.2 - - + +
122A ILE* 1.3 60.2 + - - +
124A GLN* 3.3 9.5 + - + +
125A GLU* 2.9 32.3 + - - +
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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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5A ILE* 3.8 12.3 - - + -
93A TYR* 4.0 14.3 - - + -
109A VAL* 4.1 20.6 - - + -
112A SER* 3.3 35.2 - - - +
114A HIS* 4.2 7.4 - - + -
115A CYS* 3.9 26.2 - - + +
117A GLY 4.6 1.1 - - - -
118A SER 2.9 28.6 + - - +
119A ALA 3.9 4.0 - - - +
121A LEU* 1.3 77.5 - - - +
123A ALA* 1.3 61.4 + - - +
125A GLU* 3.2 3.6 + - - +
126A ILE* 3.0 41.6 + - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.8 24.0 - - + +
7A VAL* 6.0 0.6 - - - +
119A ALA 3.0 19.4 + - - +
120A THR 3.8 3.6 - - - +
122A ILE* 1.3 76.4 - - - +
124A GLN* 1.3 62.5 + - - +
126A ILE* 3.3 7.0 + - - +
127A ARG* 3.1 29.3 + - - +
140A ALA* 4.2 7.6 - - + +
142A VAL* 3.9 16.8 - - + -
161A GLN* 3.4 12.3 - - - +
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Residues in contact with GLN 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 THR* 3.0 18.3 + - + +
121A LEU* 3.6 12.6 - - + +
123A ALA* 1.3 75.9 - - - +
125A GLU* 1.3 61.1 + - - +
127A ARG* 2.8 34.9 + - - +
128A GLN* 3.1 32.0 + - + +
161A GLN* 3.1 22.7 + - - +
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Residues in contact with GLU 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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93A TYR* 3.2 32.0 + - + +
114A HIS* 5.6 1.0 + - - +
115A CYS* 3.6 22.9 - - - -
121A LEU* 2.9 16.1 + - - +
122A ILE* 3.2 4.7 + - - +
124A GLN* 1.3 73.3 - - - +
126A ILE* 1.3 59.9 + - - +
128A GLN* 3.8 5.6 - - + +
129A THR* 2.7 37.9 + - - +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.9 2.2 - - + -
7A VAL* 4.3 12.3 - - + -
89A ILE* 4.4 4.0 - - + -
90A PHE* 3.5 31.9 - - + -
93A TYR* 3.7 29.6 - - + -
107A LEU* 3.6 30.3 - - + -
122A ILE* 3.0 37.5 + - + +
123A ALA* 3.3 8.5 + - - +
124A GLN 3.3 0.2 - - - -
125A GLU* 1.3 73.5 - - - +
127A ARG* 1.3 58.3 + - - +
129A THR* 3.3 6.3 + - - -
130A ILE* 2.9 37.1 + - + +
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Residues in contact with ARG 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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7A VAL* 5.4 2.0 - - + -
123A ALA 3.1 15.0 + - - +
124A GLN* 2.8 36.2 + - - +
126A ILE* 1.3 78.8 - - + +
128A GLN* 1.3 56.5 + - - +
130A ILE* 3.2 9.9 + - - +
131A PHE* 3.0 27.9 + - - +
136A LEU 4.9 0.7 - - - +
137A THR* 5.7 0.2 - - - -
138A ALA* 3.1 39.6 + - + +
139A SER* 3.9 3.1 - - - +
140A ALA* 3.9 16.2 - - + +
159A ASN* 2.9 35.8 + - - -
160A GLY* 3.8 28.1 + - - -
161A GLN* 3.1 16.4 + - - +
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Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN* 3.1 27.6 + - + +
125A GLU* 3.8 7.2 - - + +
127A ARG* 1.3 75.6 - - - +
129A THR* 1.3 57.5 + - - +
131A PHE* 3.2 15.0 + - - +
132A ASN* 3.0 63.1 + - - +
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.9 20.9 - - + +
92A ARG* 3.4 29.2 - - - +
93A TYR* 3.9 11.7 + - + +
125A GLU* 2.7 33.0 + - - +
126A ILE* 3.7 3.6 - - - -
128A GLN* 1.3 72.3 - - - +
130A ILE* 1.3 52.0 + - - +
132A ASN* 2.6 35.2 - - - +
133A GLU* 3.5 16.2 - - - +
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Residues in contact with ILE 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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7A VAL* 4.2 11.7 - - + -
9A MET* 3.9 23.1 - - + -
86A ILE* 4.2 21.1 - - + -
89A ILE* 4.0 23.8 - - + -
90A PHE* 3.9 16.4 - - + -
126A ILE* 2.9 38.0 + - + +
127A ARG* 3.5 5.2 - - - +
129A THR* 1.3 71.3 - - - +
131A PHE* 1.3 56.0 + - - +
132A ASN 2.6 19.2 - - - +
134A LEU* 3.1 24.5 - - + +
136A LEU 3.5 16.1 - - - +
138A ALA* 4.3 11.2 - - + -
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Residues in contact with PHE 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 ARG 3.0 16.0 + - - +
128A GLN* 3.2 15.9 + - - +
130A ILE* 1.3 72.3 - - - +
132A ASN* 1.3 71.9 + - - +
135A GLN* 2.7 43.9 + - + +
136A LEU 3.2 17.0 + - - +
137A THR* 3.8 29.6 - - + -
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Residues in contact with ASN 132 (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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128A GLN* 3.0 41.9 + - - +
129A THR* 2.6 23.8 - - - +
130A ILE 2.6 8.8 - - - +
131A PHE* 1.3 81.9 - - - +
133A GLU* 1.3 59.6 + - + +
134A LEU 2.5 16.5 + - - -
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Residues in contact with GLU 133 (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 HIS* 2.8 37.6 + - + +
89A ILE* 3.7 2.9 - - + +
92A ARG* 3.0 38.3 + - - -
129A THR* 3.5 17.2 - - + +
132A ASN* 1.3 79.3 - - + +
134A LEU* 1.3 61.3 + - + +
135A GLN* 3.9 3.7 - - - +
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Residues in contact with LEU 134 (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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19A ARG* 3.0 35.0 + - - +
81A GLU* 5.6 2.5 - - + +
82A ALA* 4.2 17.3 - - + -
85A HIS* 3.2 49.1 - - + +
86A ILE* 3.6 30.3 - - + -
89A ILE* 4.0 11.2 - - + -
130A ILE* 3.1 17.9 - - + +
132A ASN 2.5 10.3 + - - -
133A GLU* 1.3 73.8 - - - +
135A GLN* 1.3 68.3 + - - +
136A LEU* 3.2 11.2 + - + +
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Residues in contact with GLN 135 (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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19A ARG* 3.8 27.0 - - - +
25A ARG* 5.5 3.3 + - - -
131A PHE* 2.7 41.3 + - + +
133A GLU 5.5 2.7 - - - +
134A LEU* 1.3 75.8 - - - +
136A LEU* 1.3 63.0 + - - +
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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