Contacts of the strand formed by residues 163 - 170 (chain K) in PDB entry 4GUN
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 LEU 163 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148J ASP* 5.7 0.9 - - - +
138K VAL* 4.5 18.2 - - + -
139K LYS 3.5 3.1 - - - +
140K ASN* 3.6 41.3 - - + +
158K ILE* 3.6 25.0 - - + +
160K ALA* 3.1 25.5 + - + +
161K PRO 4.0 0.5 - - - +
162K HIS* 1.3 91.8 - - + +
164K VAL* 1.4 63.7 + - - +
61L LYS* 2.8 32.2 + - - -
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Residues in contact with VAL 164 (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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138K VAL* 3.3 4.1 - - - -
139K LYS* 2.9 43.8 + - + +
141K LYS* 3.7 35.2 - - + +
158K ILE* 4.4 2.5 - - - -
163K LEU* 1.4 80.0 - - - +
165K PRO* 1.4 79.5 - - + +
166K ILE* 3.3 10.8 + - + +
203K ARG* 3.8 23.1 - - + +
206K ALA* 6.3 0.4 - - + -
61L LYS* 5.5 0.7 - - - +
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Residues in contact with PRO 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K THR* 6.2 0.7 - - + -
82K LEU* 3.9 37.1 - - + +
136K PHE* 4.1 18.2 - - + -
137K ILE 4.0 4.7 - - - +
138K VAL* 4.3 6.3 - - + -
157K THR* 5.9 0.4 - - - +
158K ILE* 4.0 25.5 - - + +
163K LEU 4.2 3.1 - - - +
164K VAL* 1.4 93.8 - - + +
166K ILE* 1.3 60.9 + - - +
167K ILE 5.3 1.3 - - - +
203K ARG* 3.7 15.6 - - - +
61L LYS* 5.1 4.9 - - + +
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Residues in contact with ILE 166 (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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104K LEU* 3.9 17.7 - - + -
137K ILE* 2.8 21.4 + - + +
138K VAL 4.0 2.2 - - - -
139K LYS* 3.8 26.0 - - + +
147K LEU* 4.3 6.7 - - + -
164K VAL* 3.5 28.0 - - + +
165K PRO* 1.3 73.5 - - - +
167K ILE* 1.3 64.0 + - + +
197K TRP* 5.6 1.1 - - + -
200K ALA* 3.5 37.7 - - + +
203K ARG* 3.1 28.1 + - - +
204K TYR* 3.7 33.0 - - + +
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Residues in contact with ILE 167 (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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86K ASN* 3.5 19.3 - - + +
122K THR* 5.9 0.4 - - + -
136K PHE* 3.2 11.5 - - - +
137K ILE* 3.1 48.6 + - + +
165K PRO* 5.2 0.9 - - - -
166K ILE* 1.3 81.7 - - + +
168K ALA* 1.4 61.5 + - - +
169K ILE* 3.8 30.3 - - + -
192K TRP* 4.3 6.5 - - + -
195K ILE* 3.6 25.4 - - + -
196K ASN 4.2 2.5 - - - +
197K TRP* 3.9 23.1 - - + -
200K ALA* 3.7 22.7 - - + -
203K ARG* 4.8 0.4 - - - -
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Residues in contact with ALA 168 (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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79K ASN 4.3 0.4 - - - +
82K LEU* 3.8 25.6 - - + -
83K PHE* 3.3 13.7 - - - +
86K ASN* 2.8 32.3 + - - +
134K TRP* 4.1 14.1 - - + -
135K ALA 3.7 4.9 - - - -
136K PHE* 3.9 19.1 - - + -
165K PRO* 5.8 0.4 - - + -
167K ILE* 1.4 73.0 - - - +
169K ILE* 1.3 63.1 + - - +
203K ARG* 5.2 0.2 - - - +
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Residues in contact with ILE 169 (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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83K PHE* 4.0 2.2 - - - -
122K THR* 4.6 5.2 - - + -
126K LEU* 3.7 38.1 - - + +
134K TRP* 3.3 9.3 - - - -
135K ALA* 3.0 35.8 + - + +
167K ILE* 3.8 17.3 - - + -
168K ALA* 1.3 77.0 - - - +
170K ASP* 1.3 69.4 + - - +
171K ALA 3.6 0.3 + - - -
187K TYR* 4.8 0.4 - - - +
188K PHE* 4.6 5.2 - - + -
191K ILE* 4.2 29.2 - - + -
192K TRP* 4.2 14.8 - - + -
195K ILE* 3.5 31.9 - - + -
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Residues in contact with ASP 170 (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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32K HIS* 2.9 7.8 + - - -
80K HIS* 3.3 3.3 + - - -
83K PHE* 3.5 21.6 - - + -
134K TRP* 3.4 28.9 - - + -
169K ILE* 1.3 74.0 - - - +
171K ALA* 1.4 59.4 + - - +
172K TRP* 3.1 30.8 + - - +
175K ALA* 3.8 12.3 - - + +
187K TYR* 3.0 29.5 + - - -
301K MN 2.0 34.4 + - - -
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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