Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 2PKG
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 HIS 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A HIS* 3.6 47.5 + + + +
90A LEU* 3.7 16.3 - - + +
123A ASP* 3.0 12.1 + - - +
126A ALA* 1.3 93.0 + - + +
128A PHE* 1.3 73.3 + - - +
130A PRO* 2.9 12.5 - - - +
131A LEU* 3.1 14.6 + - - +
134A ARG* 4.5 4.1 + - - +
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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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90A LEU* 3.4 17.5 - - + +
112A LEU* 3.8 33.9 - - + -
115A ILE* 5.1 0.4 - - + -
116A SER* 3.3 33.7 - - - -
119A HIS* 3.7 21.9 - + + -
123A ASP 3.9 1.8 + - - -
124A LEU* 3.3 25.5 + - + +
127A HIS* 1.3 73.7 - - - +
129A VAL* 1.3 54.7 + - - +
130A PRO 2.6 0.9 - - - -
131A LEU* 2.5 37.1 + - + +
132A VAL* 3.1 18.5 + - + -
150A LEU* 4.1 32.1 - - + -
153A VAL* 4.3 2.9 - - + -
154A CYS* 3.8 23.3 - - + -
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Residues in contact with VAL 129 (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 LEU 3.1 11.7 + - - +
125A GLU* 4.3 6.3 - - - +
128A PHE* 1.3 77.3 - - - +
130A PRO* 1.3 72.7 - - + +
132A VAL* 3.2 12.9 + - - +
133A LYS* 3.1 34.3 + - - +
154A CYS* 3.4 34.1 - - + -
158A VAL* 4.2 6.7 - - + -
162A VAL* 3.9 27.1 - - + -
165A GLU* 4.9 4.0 - - - +
166A LEU* 4.0 15.5 - - + -
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Residues in contact with PRO 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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124A LEU 3.6 4.5 - - - +
125A GLU 4.0 7.2 - - - +
126A ALA 3.0 23.6 - - - +
127A HIS* 2.9 21.5 - - - +
128A PHE 2.6 0.8 - - - +
129A VAL* 1.3 96.1 - - + +
131A LEU* 1.3 55.4 + - - +
133A LYS* 3.0 26.2 + - + +
134A ARG* 3.0 31.4 + - - +
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Residues in contact with LEU 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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90A LEU* 3.4 23.8 - - + +
94A GLU* 3.1 51.1 - - + +
112A LEU* 4.3 18.6 - - + -
127A HIS 3.1 4.9 + - - +
128A PHE* 2.5 24.2 + - + +
130A PRO* 1.3 72.8 - - - +
132A VAL* 1.3 73.5 + - + +
134A ARG* 3.4 13.7 - - - +
135A LEU* 2.9 42.4 + - + +
150A LEU* 4.3 9.2 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.7 23.8 - - + +
129A VAL* 3.4 17.3 - - - +
130A PRO 3.1 0.2 - - - -
131A LEU* 1.3 90.5 - - + +
133A LYS* 1.3 59.4 + - + +
135A LEU* 4.3 5.1 - - - +
136A ALA* 3.2 27.0 + - - +
147A ALA* 4.4 2.7 - - + +
150A LEU* 4.1 23.3 - - + +
151A PHE* 3.3 39.9 - - + -
154A CYS* 4.9 2.0 - - - -
166A LEU* 4.7 10.8 - - + -
169A TYR* 6.2 0.7 - - + -
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Residues in contact with LYS 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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129A VAL* 3.1 21.4 + - + +
130A PRO* 3.0 12.7 + - + +
132A VAL* 1.3 77.3 - - + +
134A ARG* 1.3 61.7 + - + +
137A GLY* 3.1 24.6 + - - -
165A GLU* 2.9 43.7 + - - +
166A LEU* 5.7 2.9 - - + +
169A TYR* 3.1 60.9 + - + +
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Residues in contact with ARG 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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90A LEU* 5.6 3.8 + - - +
91A PRO* 5.8 5.7 - - - +
94A GLU* 2.8 45.1 + - - +
127A HIS* 4.5 4.6 + - - +
130A PRO* 3.0 34.1 + - - +
131A LEU* 3.1 19.5 + - - +
133A LYS* 1.3 77.2 - - + +
135A LEU* 1.3 66.7 + - - +
137A GLY 3.4 0.5 + - - -
138A GLY* 3.0 22.5 + - - -
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Residues in contact with LEU 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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94A GLU* 3.9 24.5 - - + +
97A ALA* 4.6 11.7 - - + +
98A THR* 3.5 24.5 - - - +
112A LEU* 4.4 9.2 - - + -
131A LEU* 2.9 29.3 + - + +
132A VAL* 4.3 1.3 - - - +
134A ARG* 1.3 76.1 - - - +
136A ALA* 1.3 56.9 + - - +
138A GLY* 3.0 20.3 + - - -
143A SER* 3.6 25.3 - - - +
144A ARG* 3.5 14.6 + - - +
146A SER 4.8 0.7 - - - +
147A ALA* 3.7 13.2 - - + +
150A LEU* 3.9 27.6 - - + -
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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 VAL 3.2 18.7 + - - +
133A LYS 4.4 0.2 - - - +
135A LEU* 1.3 78.7 - - - +
137A GLY* 1.3 57.1 + - - +
144A ARG* 2.8 25.9 + - - +
147A ALA* 3.6 12.0 - - + +
151A PHE* 4.6 3.1 - - + -
169A TYR* 4.1 21.0 - - + -
173A LEU* 3.9 28.4 - - + +
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Residues in contact with GLY 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 LYS 3.1 18.4 + - - -
134A ARG 3.9 0.4 - - - -
135A LEU 3.1 0.2 - - - -
136A ALA* 1.3 77.6 - - - +
138A GLY* 1.3 70.7 + - - +
144A ARG* 4.5 0.2 - - - -
169A TYR* 5.2 5.4 - - - -
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Residues in contact with GLY 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 ARG 3.0 14.5 + - - -
135A LEU 3.0 11.0 + - - -
137A GLY* 1.3 87.8 - - - +
139A ASP* 1.3 66.8 + - - +
140A TRP 3.6 1.6 - - - -
143A SER* 4.9 6.7 - - - -
144A ARG* 3.2 17.4 + - - -
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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