Contacts of the strand formed by residues 167 - 174 (chain N) in PDB entry 7K63
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 VAL 167 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159N GLU* 4.3 25.8 - - + -
161N VAL* 4.5 11.2 - - + -
166N SER* 1.3 76.5 - - - +
168N LYS* 1.3 69.7 + - - +
169N MET* 4.2 10.4 - - + +
230N MET 3.8 1.0 - - - +
231N GLU* 3.1 3.0 - - - -
232N LEU* 2.7 50.0 + - + +
235N LEU* 3.6 27.8 - - + -
265N VAL* 4.3 13.5 - - + -
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Residues in contact with LYS 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N GLU* 5.4 3.8 - - - +
166N SER* 6.1 0.2 - - - +
167N VAL* 1.3 78.4 - - - +
169N MET* 1.3 62.4 + - - +
170N PRO* 3.7 9.0 - - - +
220N THR* 4.4 8.7 + - - +
229N TYR* 3.5 43.8 - - + -
230N MET 3.3 8.1 - - - +
231N GLU* 4.0 19.1 - - + -
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Residues in contact with MET 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156N SER* 4.4 6.1 - - - +
159N GLU* 5.5 1.6 - - + -
167N VAL* 4.5 14.6 - - + -
168N LYS* 1.3 75.2 - - - +
170N PRO* 1.3 66.8 - - + +
185N TRP* 3.7 16.4 - - + -
229N TYR* 3.5 3.1 - - - -
230N MET* 2.6 52.7 + - + +
232N LEU* 3.5 37.0 - - + -
243N TYR* 3.9 31.0 - - + -
263N THR* 4.1 18.4 - - + +
265N VAL* 3.7 21.3 - - + -
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Residues in contact with PRO 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N GLN 4.0 0.8 - - - +
155N GLN* 3.8 10.7 - - - +
156N SER* 3.4 42.0 + - - +
159N GLU* 5.5 1.6 - - - +
168N LYS 3.7 8.3 - - - +
169N MET* 1.3 85.8 - - - +
171N CYS* 1.3 59.0 + - - +
172N LYS* 4.2 1.1 - - + +
185N TRP* 4.6 1.5 - - - -
227N THR* 4.3 5.6 - - + -
228N VAL 3.6 4.0 - - - +
229N TYR* 3.5 27.1 - - + -
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Residues in contact with CYS 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N LEU* 3.6 25.8 - - - -
154N GLN 3.8 3.1 - - - -
155N GLN* 5.0 0.4 - - - +
170N PRO* 1.3 74.4 - - - +
172N LYS* 1.3 61.7 + - - +
173N ALA* 3.8 2.1 + - - +
178N PHE* 5.8 0.2 - - - -
183N ILE* 4.3 7.4 - - - -
185N TRP* 3.9 13.7 - - + -
226N SER 3.6 1.2 - - - +
227N THR* 2.9 10.2 - - - -
228N VAL* 2.6 52.2 + - + +
245N CYS* 3.3 37.0 - - + -
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Residues in contact with LYS 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N GLN 3.9 1.0 - - - +
153N LEU* 3.6 1.4 - - - -
154N GLN* 2.7 58.4 + - + +
170N PRO* 4.2 1.1 - - + -
171N CYS* 1.3 72.6 - - - +
173N ALA* 1.3 72.4 + - - +
174N SER* 3.9 15.0 + - - -
225N SER* 3.5 26.0 - - - +
226N SER* 3.8 2.3 - - - +
227N THR* 3.9 8.5 - - + +
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Residues in contact with ALA 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N GLN 3.7 4.9 - - - -
153N LEU* 3.9 11.2 - - + -
171N CYS* 3.8 3.1 + - - +
172N LYS* 1.3 77.6 + - - +
174N SER* 1.3 60.9 + - - +
176N TYR* 3.4 31.4 - - + +
178N PHE* 3.7 18.7 - - + +
183N ILE* 5.0 0.7 - - + -
226N SER* 2.9 36.1 + - - +
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Residues in contact with SER 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N GLU 5.2 0.2 + - - -
152N GLN* 2.9 50.9 + - - +
154N GLN* 5.3 4.1 - - - +
172N LYS* 4.2 17.6 + - - -
173N ALA* 1.3 76.4 - - - +
175N GLY* 1.3 64.2 + - - +
176N TYR* 3.3 13.5 - - - -
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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