Contacts of the strand formed by residues 151 - 158 (chain A) in PDB entry 5GKI
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 LYS 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY 3.7 3.2 + - - +
150A PHE* 1.3 76.0 - - - +
152A PRO* 1.3 66.0 - - + +
153A LEU* 4.1 19.6 - - + +
168A GLY* 3.1 2.4 - - - -
169A ARG* 2.8 52.7 + - + +
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Residues in contact with PRO 152 (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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139A ILE* 4.2 16.2 - - + +
140A PHE* 3.7 43.3 - - + +
143A PRO* 3.7 9.4 - - + -
150A PHE* 3.3 37.9 - - + +
151A LYS* 1.3 89.2 - - + +
153A LEU* 1.3 66.9 + - - +
166A VAL* 4.4 4.7 - - + -
167A LEU 4.1 3.1 - - - +
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Residues in contact with LEU 153 (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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140A PHE* 4.0 11.9 - - - -
151A LYS* 4.1 26.7 - - + +
152A PRO* 1.3 86.1 - - - +
154A PHE* 1.3 92.7 + - + +
167A LEU* 2.8 10.5 + - + +
168A GLY* 4.0 11.2 - - - -
169A ARG* 4.0 25.4 - - + -
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Residues in contact with PHE 154 (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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140A PHE* 3.8 7.3 - - - -
153A LEU* 1.3 106.6 - - + +
155A ARG* 1.3 60.5 + - - +
156A GLU 4.3 0.2 - - - -
157A LYS* 3.4 43.1 - - + -
165A ALA 4.6 0.2 - - - -
166A VAL* 3.4 5.2 - - - -
167A LEU* 2.8 62.6 + - + +
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Residues in contact with ARG 155 (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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136A ALA* 4.0 26.5 - - + -
137A GLU* 4.8 16.4 - - - +
140A PHE* 3.8 43.4 - - + +
154A PHE* 1.3 74.2 - - - +
156A GLU* 1.3 84.7 + - + +
157A LYS* 3.2 2.1 + - - +
165A ALA 3.5 7.6 - - - +
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Residues in contact with GLU 156 (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 GLU* 4.7 13.2 - - - +
155A ARG* 1.3 83.5 - - + +
157A LYS* 1.3 61.4 + - - +
158A ALA 3.6 1.6 + - - -
163A ILE* 3.5 17.1 - - + +
164A VAL 3.3 9.8 - - - +
165A ALA* 2.9 23.7 + - - +
102C MPD 3.0 47.6 - - + +
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Residues in contact with LYS 157 (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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154A PHE* 3.4 50.3 - - + -
155A ARG* 3.2 2.2 - - - +
156A GLU* 1.3 73.3 - - - +
158A ALA* 1.3 90.8 + - - +
159A ILE* 3.2 5.0 + - + +
163A ILE* 3.7 1.8 - - - -
164A VAL* 3.1 29.4 + - + +
165A ALA 4.7 0.2 + - - -
167A LEU* 4.5 18.6 - - + -
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Residues in contact with ALA 158 (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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156A GLU 3.6 4.9 + - - -
157A LYS* 1.3 105.7 + - + +
159A ILE* 1.3 65.4 + - - +
162A GLY 3.5 9.9 - - - +
163A ILE* 3.8 16.3 - - + +
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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