Contacts of the helix formed by residues 116 - 128 (chain A) in PDB entry 3PEY
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LYS 3.6 2.0 + - - -
115A PRO* 1.3 75.9 - - - +
117A LYS* 1.3 66.6 + - - +
118A ILE* 3.4 2.5 - - - +
119A GLN* 2.9 32.1 + - - +
120A GLU* 2.9 21.3 + - - +
142A THR* 2.8 31.6 + - - -
430A PHE* 4.0 17.5 - - - -
1000A ADP 4.0 1.4 + - - -
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Residues in contact with LYS 117 (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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116A SER* 1.3 73.8 - - - +
118A ILE* 1.3 63.9 + - - +
120A GLU* 3.2 8.9 + - - +
121A ARG* 3.0 57.6 + - - +
142A THR* 6.2 2.6 - - - +
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Residues in contact with ILE 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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116A SER* 3.4 12.8 - - - +
117A LYS* 1.3 77.6 - - - +
119A GLN* 1.3 60.7 + - + +
121A ARG* 4.7 5.4 - - + +
122A ALA* 2.8 39.6 + - + +
136A ALA* 4.5 10.1 - - + -
137A GLN 4.1 10.1 - - - +
138A SER* 3.4 38.8 + - - +
142A THR* 3.5 19.3 - - - +
143A GLY 4.3 11.2 - - - -
144A LYS* 4.4 2.5 - - + +
147A ALA* 5.1 1.3 - - + -
270A PHE* 4.3 16.6 - - + -
292A LEU* 4.0 26.0 - - + -
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Residues in contact with GLN 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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94A PHE* 3.4 9.2 - - + -
115A PRO* 3.3 11.6 - - + +
116A SER* 2.9 33.4 + - - +
118A ILE* 1.3 79.8 - - + +
120A GLU* 1.3 62.1 + - - +
123A LEU* 3.0 44.5 + - + +
143A GLY* 2.9 31.4 + - - +
146A ALA* 3.6 13.1 - - + +
147A ALA* 4.2 15.7 - - + +
1000A ADP 2.9 39.7 + - - -
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Residues in contact with GLU 120 (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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91A ALA* 3.2 41.6 + - + +
97A LEU* 4.3 13.2 - - + +
115A PRO* 4.1 17.6 - - + +
116A SER 2.9 15.6 + - - +
117A LYS* 3.2 9.7 + - - +
119A GLN* 1.3 77.5 - - - +
121A ARG* 1.3 61.1 + - + +
124A PRO* 3.0 25.3 - - - +
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Residues in contact with ARG 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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117A LYS* 3.0 45.2 + - - +
118A ILE* 4.1 5.4 - - - +
120A GLU* 1.3 81.6 - - + +
122A ALA* 1.3 64.0 + - - +
124A PRO* 3.6 6.4 - - - +
125A LEU* 3.5 22.2 - - - +
292A LEU* 4.3 24.0 - - + -
294A LEU* 6.3 0.8 - - - +
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Residues in contact with ALA 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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118A ILE* 2.8 26.4 + - + +
121A ARG* 1.3 75.3 - - - +
123A LEU* 1.3 59.3 + - - +
125A LEU* 3.2 3.3 + - - +
126A LEU* 2.8 47.1 + - + +
134A MET* 4.3 4.7 - - + -
147A ALA* 4.6 4.9 - - + -
270A PHE* 4.2 15.5 - - + -
292A LEU* 3.8 21.1 - - + -
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Residues in contact with LEU 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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94A PHE* 4.4 3.4 - - + -
97A LEU* 3.9 27.8 - - + -
99A LEU* 4.8 5.2 - - + -
119A GLN* 3.0 34.9 + - + +
122A ALA* 1.3 76.2 - - - +
124A PRO* 1.4 67.0 - - + +
126A LEU* 3.1 3.5 + - + +
127A LEU* 2.9 46.0 + - + +
147A ALA* 3.5 31.9 - - - +
150A LEU* 4.1 33.9 - - + -
151A THR* 3.7 10.8 - - - +
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Residues in contact with PRO 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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97A LEU* 4.1 19.7 - - + +
120A GLU 3.0 29.2 - - - +
121A ARG 3.6 7.0 - - - +
123A LEU* 1.4 89.7 - - + +
125A LEU* 1.3 58.4 + - + +
127A LEU* 4.2 5.1 - - + +
128A HIS* 3.0 30.8 + - - +
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Residues in contact with LEU 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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121A ARG* 3.5 18.6 - - - +
122A ALA 3.2 6.6 + - - +
124A PRO* 1.3 79.3 - - + +
126A LEU* 1.3 62.0 + - - +
127A LEU 3.7 0.2 + - - -
128A HIS* 3.7 16.2 - - + +
132A ARG 4.7 7.6 + - - +
134A MET* 3.6 23.8 - - + -
266A GLN* 4.7 0.5 + - - -
290A ASN* 3.7 36.8 + - + +
292A LEU* 4.2 19.3 - - + -
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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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122A ALA* 2.8 35.5 + - + +
123A LEU* 3.6 3.8 - - - +
125A LEU* 1.3 79.0 - - - +
127A LEU* 1.3 57.8 + - - +
134A MET* 3.6 33.7 - - + -
147A ALA 4.0 10.8 - - - +
148A PHE* 4.8 0.9 - - - -
151A THR* 3.4 34.9 - - + +
155A ARG* 2.9 22.7 + - - -
266A GLN* 3.1 19.7 + - - +
268A VAL* 3.8 23.6 - - + -
270A PHE* 4.0 16.6 - - + -
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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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97A LEU 3.5 24.5 - - - +
98A GLY* 4.8 6.7 - - - +
99A LEU* 4.0 19.3 - - + -
123A LEU* 2.9 31.5 + - + +
124A PRO* 4.2 3.4 - - + +
126A LEU* 1.3 74.4 - - - +
128A HIS* 1.3 67.5 + - - +
129A ASN* 3.5 9.2 + - - +
150A LEU 4.7 0.7 - - - +
151A THR* 4.1 23.1 - - + +
154A THR* 3.7 37.2 - - + +
155A ARG* 3.4 13.5 + - - +
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Residues in contact with HIS 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 PRO 3.0 18.0 + - - +
125A LEU* 3.7 13.0 - - + +
126A LEU 3.4 1.5 - - - +
127A LEU* 1.3 76.1 - - - +
129A ASN* 1.3 77.4 + - - +
130A PRO* 3.2 31.8 + - + +
131A PRO* 3.5 10.9 - - - +
132A ARG* 4.6 10.8 + - + -
155A ARG* 2.9 19.1 + - - -
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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