Contacts of the strand formed by residues 139 - 150 (chain C) in PDB entry 4KG8
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 GLY 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C LYS 3.6 3.0 + - - -
138C ALA* 1.3 74.8 - - - +
140C TYR* 1.3 63.9 + - - -
141C TYR* 3.3 12.6 - - - -
208C HIS* 3.5 17.0 - - - -
209C LEU 2.9 32.0 + - - -
239C MET* 4.7 6.5 - - - -
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Residues in contact with TYR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 5.8 3.8 - - + -
122A PHE* 3.6 46.2 - + + +
124A ARG* 2.5 53.0 + - - -
139C GLY* 1.3 74.7 - - - -
141C TYR* 1.3 60.9 + - - +
206C VAL* 3.9 10.8 - - + -
207C VAL 3.4 2.5 - - - -
208C HIS* 3.5 45.3 - + + -
239C MET* 3.2 9.9 - - - +
240C VAL* 3.0 38.4 + - + +
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Residues in contact with TYR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PRO* 4.2 12.6 - - + +
125C GLY 5.0 0.3 + - - -
126C LEU* 3.8 23.2 - - + +
135C VAL* 3.5 18.6 - - + +
137C LYS* 2.3 42.7 + - - +
139C GLY* 3.3 23.8 - - - -
140C TYR* 1.3 75.8 - - - +
142C TYR* 1.3 61.6 + - - +
143C ILE* 3.6 17.0 + - + -
205C GLY 3.5 0.7 - - - +
206C VAL* 3.2 4.6 - - - -
207C VAL* 2.8 36.1 + - - +
209C LEU* 4.0 16.6 - - + -
237C ALA* 4.5 7.9 - - + -
238C PHE* 3.4 11.9 - - - +
239C MET* 3.8 31.6 - - + -
240C VAL 4.6 0.2 - - - +
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Residues in contact with TYR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.0 38.5 + + - -
144A TYR* 4.3 5.8 - + - -
202A PHE* 3.8 6.9 - - - -
238A PHE* 3.7 16.8 - + + -
142B TYR* 3.1 29.3 + + - -
141C TYR* 1.3 71.0 - - - +
143C ILE* 1.3 59.9 + - - +
144C TYR* 4.1 14.8 - + + -
202C PHE* 4.0 1.9 - - - -
204C GLY* 3.7 17.5 - - - -
205C GLY* 3.3 33.2 - - - -
206C VAL* 3.8 10.2 - - + +
237C ALA* 3.0 4.0 - - - -
238C PHE* 2.9 70.4 + + + +
240C VAL* 4.2 3.3 - - + +
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LEU* 6.0 0.4 - - + -
141C TYR* 4.0 17.0 - - + +
142C TYR* 1.3 77.1 - - - +
144C TYR* 1.3 61.4 + - - +
166C LEU* 3.9 30.3 - - + -
179C LEU* 4.1 14.4 - - + -
180C LEU* 3.9 12.1 - - + +
204C GLY* 3.2 2.4 - - - -
205C GLY 2.8 41.3 + - - +
207C VAL* 3.8 24.7 - - + -
209C LEU* 4.6 7.6 - - + -
215C VAL* 4.3 14.1 - - + -
235C PHE* 5.5 0.9 - - + -
236C GLY 3.4 6.7 - - - +
237C ALA* 3.8 18.4 - - + -
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TYR* 4.4 4.3 - + - -
204B GLY 4.0 5.6 - - - -
205B GLY* 3.4 21.1 - - - -
206B VAL* 2.8 26.4 + - + +
96C ALA 3.9 0.5 + - - -
97C HIS* 2.6 29.5 + - - +
142C TYR* 4.1 18.8 - + + -
143C ILE* 1.3 77.8 - - - +
145C SER* 1.3 64.5 + - - +
166C LEU* 4.2 5.7 - - - +
202C PHE* 3.9 13.9 - + + -
203C LEU 3.1 13.9 - - - +
204C GLY* 4.1 3.1 - - - -
234C TYR* 3.5 33.4 - + - -
235C PHE* 3.5 2.8 - - - -
236C GLY* 2.8 60.1 + - - +
237C ALA* 3.6 5.8 - - - -
238C PHE* 4.7 0.7 - + - -
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C TYR* 1.3 79.7 - - - +
146C LYS* 1.3 62.7 + - - +
147C VAL* 4.2 1.0 - - - +
164C HIS* 2.9 29.3 + - - -
166C LEU* 4.1 11.8 - - - +
202C PHE* 3.4 3.0 - - - -
203C LEU 2.8 32.9 + - - -
217C VAL* 3.6 27.8 - - - +
234C TYR 3.2 16.5 + - - -
235C PHE* 4.3 0.2 - - - -
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B VAL 2.7 29.1 + - - -
202B PHE 5.0 0.2 - - - +
203B LEU* 4.0 13.9 - - + -
145C SER* 1.3 74.8 + - - +
147C VAL* 1.3 65.5 + - - +
148C GLN* 3.9 14.3 + - - +
200C SER* 3.2 22.9 - - - +
201C SER 3.1 10.1 - - - +
202C PHE* 3.9 14.6 - - + +
232C ARG* 2.8 38.2 + - - +
233C SER* 3.2 3.9 - - - +
234C TYR* 2.9 69.6 + - + +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 4.7 10.5 - - + -
114C TRP* 4.7 5.6 - - + -
145C SER* 4.2 3.8 - - - +
146C LYS* 1.3 82.5 - - - +
148C GLN* 1.3 61.4 + - - +
149C LEU* 3.6 30.5 + - + +
164C HIS* 3.7 37.7 - - + +
200C SER* 3.4 1.4 - - - -
201C SER* 2.7 36.6 + - - +
217C VAL* 4.6 8.5 - - + -
219C VAL* 4.7 12.6 - - + -
233C SER* 3.4 12.1 - - - +
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B VAL 4.1 1.0 - - - +
182B SER* 3.4 11.6 - - - -
183B GLN* 2.9 59.6 + - - +
146C LYS* 3.9 8.8 + - - +
147C VAL* 1.3 74.3 - - - +
149C LEU* 1.3 80.0 + - - +
198C PHE* 4.0 6.9 - - + +
199C ASP 3.2 17.5 + - - -
200C SER* 4.3 3.3 - - - +
232C ARG* 3.9 26.1 - - + +
233C SER* 2.9 16.6 + - - +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C VAL* 3.6 25.8 - - + +
148C GLN* 1.3 90.4 + - - +
150C GLY* 1.3 57.1 + - - +
162C ILE* 3.9 33.2 - - + -
164C HIS* 6.2 1.1 - - + -
184C GLN* 5.5 5.2 - - + +
186C PRO* 6.1 0.7 - - + -
197C TRP* 3.9 13.2 - - + -
198C PHE* 3.2 7.1 - - - +
199C ASP* 2.5 56.7 + - + +
201C SER* 4.8 12.1 - - - -
219C VAL* 4.5 13.9 - - + -
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Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 1.3 76.9 - - - +
151C GLY* 1.3 57.5 + - - -
197C TRP* 2.9 25.1 - - - -
198C PHE* 4.2 8.3 - - - -
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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