Contacts of the strand formed by residues 152 - 159 (chain K) in PDB entry 1P7G
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 GLN 152 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15J THR* 3.5 15.4 - - - +
16J LYS* 2.8 51.1 + - + +
18J TYR* 2.8 33.3 + - - +
58J LEU* 3.7 6.5 - - - +
118K PHE* 3.5 22.1 - - + -
146K TYR* 3.8 6.8 - - - -
147K GLU* 2.8 32.7 + - + +
150K GLU* 4.4 1.3 - - - +
151K GLU* 1.3 75.6 - - - +
153K LEU* 1.3 68.5 + - - +
154K LEU* 4.0 18.3 - - + +
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Residues in contact with LEU 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J ARG* 4.5 3.1 + - - -
111K ILE* 4.7 3.8 - - + -
114K LEU* 3.5 45.5 - - + +
115K ILE* 3.8 12.8 - - + +
118K PHE* 3.6 25.3 - - + +
119K PHE* 3.9 30.1 - - + -
144K LEU* 4.2 8.5 - - + -
145K VAL 3.4 6.1 - - - +
146K TYR* 4.2 13.7 - - + -
152K GLN* 1.3 76.9 - - - +
154K LEU* 1.3 72.6 + - - +
172K LEU* 3.7 30.1 - - + -
210K LEU* 4.5 0.9 - - + -
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Residues in contact with LEU 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J TYR* 4.2 6.7 - - - +
58J LEU* 3.9 25.8 - - + -
65J ARG* 4.5 12.8 - - - +
80J LEU* 4.2 20.4 - - + -
84J LEU* 3.9 18.4 - - + -
119K PHE* 4.9 2.5 - - - -
144K LEU* 3.5 2.9 - - - +
145K VAL* 2.7 52.9 + - + +
147K GLU* 3.8 29.4 - - + -
152K GLN* 4.0 13.9 - - + -
153K LEU* 1.3 83.4 - - - +
155K ILE* 1.3 67.4 + - - +
156K LEU* 5.0 3.4 - - + -
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Residues in contact with ILE 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J LEU* 5.7 0.3 - - - +
65J ARG* 4.9 0.8 - - - +
77J LEU* 3.3 36.5 - - + +
80J LEU* 4.5 1.2 - - - +
119K PHE* 3.8 13.2 - - + -
125K PHE* 3.6 32.3 - - + -
128K GLU* 3.8 27.7 + - + +
129K PHE* 3.5 39.5 - - + +
132K ALA* 3.9 17.5 - - + -
142K ALA* 5.4 0.4 - - + -
143K ILE 3.3 9.4 - - - +
144K LEU* 4.1 5.2 - - + -
154K LEU* 1.3 77.6 - - - +
156K LEU* 1.3 71.6 + - - +
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Residues in contact with LEU 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J LEU* 3.9 22.2 - - + +
80J LEU* 4.0 24.9 - - + -
81J SER* 4.5 8.3 - - - +
84J LEU* 5.6 1.8 - - + -
132K ALA* 4.9 0.2 - - - +
142K ALA* 3.5 4.2 - - - -
143K ILE* 2.8 43.2 + - + +
145K VAL* 4.7 20.0 - - + -
154K LEU* 5.0 5.2 - - + -
155K ILE* 1.3 86.0 - - - +
157K GLN* 1.3 64.7 + - - +
158K ILE* 4.8 1.8 - - + -
164K MSE 3.2 25.1 - - - +
165K HIS* 4.3 2.7 - - - -
166K ALA* 3.8 28.3 - - + +
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Residues in contact with GLN 157 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73J ILE 4.9 0.7 - - - -
74J ARG* 3.3 44.7 + - - +
77J LEU* 3.9 13.2 - - + +
78J ARG* 4.9 0.6 - - - +
132K ALA* 2.9 42.8 - - + +
135K ASN* 3.0 22.3 - - - +
136K VAL* 3.7 15.9 - - + +
141K TRP 3.7 2.7 - - - +
142K ALA* 5.4 0.2 - - - -
156K LEU* 1.3 76.8 - - - +
158K ILE* 1.3 62.0 + - - +
159K GLU* 5.0 2.8 + - + +
164K MSE 2.9 48.9 - - + +
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Residues in contact with ILE 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K LEU* 5.3 0.2 - - + -
136K VAL* 4.1 4.2 - - - +
140K GLY* 3.1 2.9 - - - -
141K TRP* 2.9 43.9 + - + +
143K ILE* 3.8 32.5 - - + -
156K LEU* 4.8 2.5 - - + -
157K GLN* 1.3 81.9 - - - +
159K GLU* 1.3 66.0 + - - +
160K LYS 4.1 2.0 - - - +
161K HIS* 3.5 36.3 - - - +
163K LEU 3.2 8.3 - - - +
164K MSE 3.6 2.9 - - - +
165K HIS* 3.4 50.7 - - + +
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Residues in contact with GLU 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I LYS* 3.0 26.6 + - - +
74J ARG* 4.8 1.2 - - - -
78J ARG* 2.7 36.8 + - - -
136K VAL* 4.5 7.4 - - + -
137K GLU* 3.6 24.4 + - - +
139K VAL 3.5 4.3 - - - +
157K GLN* 5.0 1.6 + - + +
158K ILE* 1.3 75.3 - - - +
160K LYS* 1.3 76.7 + - + +
161K HIS 3.1 1.9 + - - -
162K ASN 3.4 0.3 + - - -
163K LEU* 3.2 46.3 + - + +
164K MSE 4.2 15.9 - - + +
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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