Contacts of the strand formed by residues 149 - 154 (chain P) in PDB entry 6F0X
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 ARG 149 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147P VAL* 3.2 1.5 - - - +
148P PRO* 1.3 96.2 - - + +
150P VAL* 1.3 64.6 + - - +
166P GLU* 2.3 43.6 + - + +
167P LEU 3.5 6.1 - - - +
168P ASP* 3.9 17.0 - - - +
170P SER* 5.0 1.8 - - - -
215P ALA* 3.1 4.9 - - - +
216P GLN* 3.1 29.1 + - - +
234P VAL* 3.8 31.4 - - - +
262P TRP* 3.4 25.0 - - + -
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Residues in contact with VAL 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P THR* 3.9 36.6 - - + +
138P LEU* 5.9 1.1 - - + -
142P PHE* 4.1 9.0 - - + -
147P VAL* 3.6 18.8 - - + -
149P ARG* 1.3 77.4 - - - +
151P LEU* 1.3 72.4 + - - +
152P ILE* 4.6 5.4 - - + -
165P TYR 3.8 0.6 - - - +
166P GLU* 3.5 1.0 - - - +
167P LEU* 2.9 47.9 + - + +
169P LEU* 4.3 4.9 - - + -
213P VAL* 4.0 15.5 - - + -
214P MET 3.2 10.5 - - - +
215P ALA* 3.7 7.4 - - + -
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150P VAL* 1.3 78.5 - - - +
152P ILE* 1.3 63.6 + - - +
153P LEU* 5.4 9.6 - - + -
164P PHE* 5.2 8.5 - - + -
165P TYR 3.6 2.2 - - - +
166P GLU* 4.0 28.3 - - + -
212P VAL 4.6 0.2 - - - -
213P VAL* 3.1 7.3 - - - +
214P MET* 2.3 63.2 + - + +
232P TYR* 3.3 35.7 - - + +
234P VAL* 4.5 11.7 - - + -
235P PRO* 5.7 0.2 - - + -
262P TRP* 3.5 36.3 - - + -
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Residues in contact with ILE 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P THR* 5.3 3.6 - - + +
76P LEU* 5.5 4.0 - - + -
77P LEU* 3.5 50.7 - - + +
80P ILE* 4.5 20.0 - - + -
81P MET* 5.5 1.1 - - + -
150P VAL* 4.6 8.3 - - + -
151P LEU* 1.3 80.5 - - - +
153P LEU* 1.3 72.7 + - - +
154P LEU* 4.2 8.3 - - + +
164P PHE* 3.3 4.9 - - - +
165P TYR* 2.9 42.6 + - + +
167P LEU* 5.9 3.8 - - + -
211P THR* 4.3 6.1 - - + -
212P VAL 3.4 2.9 - - - -
213P VAL* 3.6 22.4 - - + -
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Residues in contact with LEU 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P LEU* 5.4 8.1 - - + -
152P ILE* 1.3 77.5 - - - +
154P LEU* 1.3 69.3 + - - +
155P GLY 4.5 7.9 - - - +
157P ASN 3.2 25.4 - - - +
158P ALA* 3.9 19.1 - - - +
161P PRO* 3.7 15.7 - - + -
163P GLU 3.7 0.9 - - - -
164P PHE* 3.5 26.0 - - + -
211P THR* 3.3 27.4 - - - +
212P VAL* 2.5 33.7 + - + +
214P MET* 4.8 11.9 - - + -
232P TYR* 5.3 7.6 - - - +
235P PRO* 5.8 3.8 - - + -
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Residues in contact with LEU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P ILE* 5.1 4.5 - - + -
84P ARG* 3.8 26.2 - - + +
86P GLN* 4.3 14.8 - - + +
152P ILE* 4.2 13.9 - - + +
153P LEU* 1.3 82.5 - - - +
155P GLY* 1.3 53.1 + - - +
162P LYS* 2.7 36.2 + - - +
163P GLU* 2.8 54.6 + - + +
165P TYR* 4.3 17.0 - - + -
209P MET* 4.6 13.7 - - + -
210P GLY 3.1 6.3 - - - +
211P THR* 4.5 8.5 - - + +
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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