Contacts of the helix formed by residues 121 - 138 (chain A) in PDB entry 5JGH
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 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LYS* 4.3 2.9 - - - +
119A PRO 3.8 1.4 + - - -
120A ALA* 1.3 77.6 - - - +
122A PRO* 1.3 79.1 - - - +
123A PHE 3.4 2.5 - - - -
124A ILE* 3.1 21.6 + - - +
125A LYS* 3.4 6.9 + - - +
169A TYR* 3.9 6.7 - - - -
4B A 5.6 1.6 - - - -
5B T 4.5 13.5 - - - -
19C T 4.0 11.8 + - - -
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Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA 3.9 0.2 - - - -
121A GLY* 1.3 80.5 - - - +
123A PHE* 1.3 64.3 + - - +
124A ILE 3.1 0.7 + - - -
125A LYS* 3.1 10.1 + - + +
126A TYR* 3.1 19.6 + - - +
154A TRP* 3.8 21.5 - - + -
165A TYR* 4.0 21.9 - - + +
166A ILE* 4.1 12.8 - - + +
169A TYR* 3.7 33.6 - - + -
5B T 3.9 34.5 - - - +
6B T 4.8 1.6 - - - +
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLY 3.4 0.6 - - - -
122A PRO* 1.3 79.9 - - - +
124A ILE* 1.3 66.2 + - + +
126A TYR* 3.3 1.4 + + - +
127A ALA* 2.8 25.3 + - - +
147A MET* 3.4 30.5 - - + -
150A ILE* 3.4 44.9 - - + -
151A GLY* 3.5 21.3 - - - -
154A TRP* 3.4 40.6 - + + -
3B T 3.7 19.5 - - + -
4B A 3.2 38.6 + - - +
5B T 4.9 2.5 + - - +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.9 12.3 - - + -
121A GLY* 3.1 13.6 + - - +
123A PHE* 1.3 84.0 - - + +
125A LYS* 1.3 58.7 + - + +
127A ALA* 3.2 4.6 + - - +
128A ASN* 2.9 34.6 + - - +
147A MET* 4.9 1.8 - - + -
3B T 3.9 11.0 - - - +
4B A 4.4 12.8 - - + +
19C T 3.8 23.1 - - + +
20C A 3.1 69.1 - - + +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO* 4.7 1.4 - - - +
120A ALA* 3.7 40.8 + - + +
121A GLY 3.4 5.5 + - - +
122A PRO* 3.1 10.3 + - + +
124A ILE* 1.3 73.5 - - + +
126A TYR* 1.3 67.6 + - - +
128A ASN* 3.3 11.0 + - - +
129A GLU* 3.0 30.1 + - - +
165A TYR* 4.1 9.9 - - + +
168A GLU* 3.3 30.1 + - - +
169A TYR* 4.6 9.9 - - - +
172A ALA* 4.1 22.6 - - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO 3.1 6.6 + - - +
123A PHE* 3.5 7.2 - + - +
125A LYS* 1.3 75.4 - - - +
127A ALA* 1.3 65.1 + - - +
129A GLU* 3.0 5.0 + - + +
130A VAL* 3.0 41.8 + - + +
150A ILE* 3.8 24.7 - - + -
153A LYS* 3.4 30.8 + - + +
154A TRP* 3.6 51.4 - + + -
157A LEU* 3.6 34.6 - - + +
161A ILE* 5.6 0.7 - - + -
165A TYR* 3.5 34.3 - + + -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 2.8 22.3 + - + +
124A ILE* 3.2 6.9 + - + +
126A TYR* 1.3 72.5 - - - +
128A ASN* 1.3 61.5 + - - +
130A VAL* 3.6 0.9 - - - +
131A ARG* 2.8 35.7 + - + +
147A MET* 3.7 34.3 - - + -
150A ILE* 3.7 23.3 - - + +
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Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 2.9 34.9 + - - +
125A LYS* 3.8 9.3 - - - +
126A TYR 3.2 0.4 - - - -
127A ALA* 1.3 81.2 - - - +
129A GLU* 1.3 62.8 + - + +
131A ARG* 3.6 17.2 + - - +
132A SER* 4.7 3.3 + - - -
20C A 3.6 23.4 + - - +
21C A 3.6 31.4 + - - +
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 3.0 16.0 + - + +
126A TYR* 3.0 4.1 + - + +
128A ASN* 1.3 77.9 - - + +
130A VAL* 1.3 60.7 + - + +
131A ARG 3.7 0.2 + - - -
132A SER* 4.6 7.4 + - - -
133A GLN* 5.3 0.5 + - - +
165A TYR* 2.4 46.0 + - - +
168A GLU* 5.1 5.9 - - - +
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Residues in contact with VAL 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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126A TYR* 3.0 49.3 + - + +
127A ALA 3.7 3.6 - - - +
129A GLU* 1.3 74.9 - - + +
131A ARG* 1.3 67.1 + - - +
132A SER 3.3 2.7 - - - -
133A GLN* 3.2 17.0 + - + +
134A VAL* 3.0 40.1 + - + +
150A ILE* 4.0 10.8 - - + -
153A LYS* 4.1 14.4 - - - +
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA 2.8 20.3 + - - +
128A ASN* 3.8 13.2 - - - +
129A GLU 3.4 1.8 - - - -
130A VAL* 1.3 77.4 - - - +
132A SER* 1.3 70.2 + - - +
134A VAL* 3.2 1.2 + - - +
135A PHE* 2.8 58.7 + - - +
143A GLN* 3.5 31.5 + - - +
146A LEU* 3.4 26.6 - - + +
147A MET* 5.5 1.3 - - - -
150A ILE* 4.0 16.8 - - + -
21C A 4.6 15.7 - - - -
22C A 4.1 23.9 + - - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASN 4.7 2.8 + - - -
129A GLU 4.6 6.2 + - - -
130A VAL 3.3 0.6 - - - -
131A ARG* 1.3 86.5 + - - +
133A GLN* 1.3 64.2 + - - +
135A PHE* 3.3 6.5 + - - +
136A ALA* 3.1 21.7 + - - +
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Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU 5.3 0.4 + - - -
130A VAL* 3.2 20.3 + - + +
132A SER* 1.3 77.5 - - - +
134A VAL* 1.3 65.6 + - + +
136A ALA* 3.1 16.8 + - + +
137A GLN* 3.1 38.9 + - - +
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Residues in contact with VAL 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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130A VAL* 3.0 29.4 + - + +
131A ARG 3.8 2.5 - - - +
133A GLN* 1.3 74.9 - - + +
135A PHE* 1.3 63.5 + - - +
137A GLN* 3.1 22.1 + - + +
138A HIS* 3.1 17.2 + - + +
146A LEU* 4.0 15.5 - - + -
149A ILE* 3.9 27.4 - - + -
150A ILE* 4.0 16.4 - - + -
153A LYS* 3.6 32.8 - - + +
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Residues in contact with PHE 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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131A ARG* 2.8 42.3 + - - +
132A SER* 3.8 4.7 - - - +
134A VAL* 1.3 76.5 - - - +
136A ALA* 1.3 65.5 + - - +
138A HIS 3.0 30.1 - - - -
139A PRO* 3.2 35.7 - - + +
141A LYS 4.4 11.4 - - - -
146A LEU* 3.5 24.0 - - + +
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Residues in contact with ALA 136 (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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132A SER 3.1 11.2 + - - +
133A GLN* 3.1 12.6 + - + +
135A PHE* 1.3 79.5 - - - +
137A GLN* 1.3 64.7 + - - +
139A PRO* 3.5 14.8 - - - +
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Residues in contact with GLN 137 (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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133A GLN* 3.1 48.1 + - - +
134A VAL* 3.3 15.1 - - + +
136A ALA* 1.3 77.3 - - - +
138A HIS* 1.3 79.9 + - + +
139A PRO* 3.4 7.5 - - - +
153A LYS* 5.9 3.2 - - - +
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Residues in contact with HIS 138 (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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134A VAL* 3.1 21.6 + - + +
135A PHE* 3.0 19.7 + - - +
137A GLN* 1.3 95.4 - - + +
139A PRO* 1.3 60.5 - - - +
140A ASP* 3.2 18.0 + - - +
141A LYS* 3.6 39.3 + - + +
146A LEU* 4.0 5.4 - - + +
149A ILE* 4.1 21.3 - - + +
155J GLN* 2.9 33.9 + - + -
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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