Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 6JKG
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLN 2.9 11.3 + - - +
139A LYS* 3.1 9.9 - - + +
140A LEU 2.9 25.3 + - - -
187A ASN* 3.3 17.0 - - - +
189A PRO* 3.8 26.2 - - + +
192A ASN* 4.7 15.0 - - - +
193A PHE* 1.3 78.7 - - - +
195A THR* 1.3 64.4 + - - +
254A LEU* 3.3 50.6 - - + +
255A SER* 5.4 0.7 - - - -
258A SER* 3.5 28.7 - - - +
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Residues in contact with THR 195 (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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129A ILE* 6.2 0.2 - - + -
140A LEU* 3.3 15.9 - - + -
183A VAL* 2.9 34.5 + - + +
184A LEU* 4.0 3.2 - - - -
186A ALA* 3.5 7.2 - - + +
187A ASN* 3.5 21.0 + - - +
193A PHE* 3.4 34.1 - - + -
194A LEU* 1.3 79.2 - - - +
196A THR* 1.3 66.4 + - - +
254A LEU* 4.1 2.7 - - - +
261A GLY* 3.3 1.6 - - - -
262A GLY 2.9 26.9 + - - -
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Residues in contact with THR 196 (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 LEU 3.0 5.5 + - - +
141A ILE* 3.8 23.4 - - - +
142A LEU* 2.7 32.8 + - - +
183A VAL* 3.8 2.9 - - - +
184A LEU* 3.7 11.2 - - - -
195A THR* 1.3 76.1 - - - +
197A ALA* 1.3 58.9 + - - +
198A ILE* 4.6 8.3 - - - +
250A ALA* 4.7 8.2 - - + +
254A LEU* 4.1 12.9 - - + +
260A LEU* 3.1 38.6 - - + +
263A LYS 3.6 8.1 - - - +
265A PHE* 4.9 5.4 - - + -
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Residues in contact with ALA 197 (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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142A LEU* 3.1 14.6 - - + -
144A SER* 2.8 26.0 - - - +
180A GLU* 3.6 24.7 - - + +
183A VAL* 5.1 0.2 - - + -
184A LEU* 3.8 8.3 - - + +
196A THR* 1.3 75.7 - - - +
198A ILE* 1.3 65.7 + - - +
263A LYS 3.5 5.2 + - - +
264A ALA* 3.3 5.1 - - + +
265A PHE 3.0 23.0 + - - -
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Residues in contact with ILE 198 (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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141A ILE* 4.2 9.4 - - + -
142A LEU 2.9 4.4 + - - -
143A THR 3.3 0.5 - - - -
144A SER* 2.3 37.7 + - - -
196A THR* 4.6 5.8 - - - +
197A ALA* 1.3 82.4 - - - +
199A ARG* 1.3 58.9 + - - +
200A PRO* 3.2 3.5 - - + +
243A VAL 5.7 0.7 - - - +
246A GLY* 5.5 0.7 - - - -
247A HIS* 3.8 48.2 - - + +
250A ALA* 4.3 17.3 - - + -
265A PHE* 3.8 24.2 - - + -
267A ILE* 4.3 14.8 - - + -
215B LEU* 3.4 28.9 - - + -
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Residues in contact with ARG 199 (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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144A SER* 3.5 21.1 - - - -
145A SER 3.6 8.7 - - - +
146A ALA* 3.6 19.2 - - - +
148A VAL* 3.2 20.2 + - - +
149A ILE* 4.5 10.7 - - - +
180A GLU* 2.4 34.9 + - - +
184A LEU* 5.3 0.2 - - - +
197A ALA 5.2 0.2 - - - +
198A ILE* 1.3 71.8 - - - +
200A PRO* 1.3 66.3 - - - +
264A ALA* 3.3 18.0 - - + +
265A PHE 2.8 19.8 + - - +
266A HIS* 3.3 34.2 + - - +
267A ILE* 4.3 7.0 + - - +
218B ALA* 3.3 30.7 + - - +
219B ALA 5.6 0.6 + - - -
220B ARG* 5.5 6.9 - - - +
269B GLU* 4.4 2.6 - - - +
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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