Contacts of the strand formed by residues 209 - 219 (chain A) in PDB entry 1OOA
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 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE* 4.7 1.3 - - - -
100A ASN* 3.5 43.1 + - + +
107A HIS* 3.2 11.8 + - - -
206A ASP* 3.2 40.1 + - + +
207A LEU 3.5 0.6 - - - -
208A SER* 1.3 89.0 - - - +
210A VAL* 1.3 65.2 + - - +
236A ALA* 4.0 8.3 - - + -
237A ILE 3.5 8.3 - - - +
238A TYR* 3.6 31.0 - - + -
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Residues in contact with VAL 210 (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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55A PHE* 4.2 12.1 - - + -
97A LEU* 3.9 26.9 - - + -
98A VAL 3.5 8.5 - - - +
100A ASN* 5.3 1.3 - - - -
107A HIS* 3.5 38.6 - - + +
109A HIS* 4.8 2.2 - - - +
139A ILE* 3.6 32.5 - - + -
209A VAL* 1.3 73.7 - - - +
211A ARG* 1.3 70.9 + - - +
236A ALA* 3.6 0.5 - - - -
237A ILE* 2.8 37.8 + - + +
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Residues in contact with ARG 211 (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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97A LEU* 3.3 6.4 - - - +
98A VAL* 2.7 44.5 + - + +
99A THR 3.5 18.2 - - - +
100A ASN* 3.4 28.9 + - + +
101A GLY 5.1 4.8 + - - -
104A ILE* 4.4 14.5 - - - +
210A VAL* 1.3 81.0 - - - +
212A LEU* 1.3 66.8 + - - +
233A VAL* 3.8 21.6 + - + +
234A SER 2.8 31.4 + - - +
235A ASP* 4.2 12.7 + - - +
236A ALA* 3.9 11.9 - - + -
237A ILE* 4.8 1.6 - - - -
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 4.2 13.2 - - + -
67A LEU* 3.9 25.4 - - + -
80A PRO* 4.4 8.5 - - + -
95A VAL* 4.1 6.5 - - + -
96A GLN 3.5 2.0 - - - -
97A LEU* 3.4 28.9 - - + -
98A VAL* 4.6 0.9 - - - -
111A LEU* 4.2 14.1 - - + -
137A LEU* 5.0 4.7 - - + -
139A ILE* 5.4 0.4 - - + -
211A ARG* 1.3 73.9 - - - +
213A MET* 1.3 60.4 + - - +
214A PHE* 3.9 29.7 - - + -
232A VAL 4.1 0.5 - - - +
233A VAL* 3.3 3.1 - - - +
234A SER* 2.7 39.9 + - - +
237A ILE* 3.7 21.8 - - + -
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Residues in contact with MET 213 (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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94A ILE 3.6 1.4 - - - +
95A VAL* 3.5 3.4 - - - +
96A GLN* 2.9 37.5 + - + +
98A VAL* 4.0 17.0 - - + -
104A ILE* 4.8 1.8 - - - -
164A ASN* 3.8 27.6 - - + +
167A LEU* 5.0 6.5 - - + -
168A LEU* 3.5 43.1 - - + -
212A LEU* 1.3 75.1 - - - +
214A PHE* 1.3 64.6 + - - +
215A THR* 4.0 1.5 + - - +
231A PRO* 4.0 26.7 - - + -
232A VAL 3.6 4.0 - - - +
233A VAL* 3.5 28.0 - - + +
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Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.1 18.6 - - + +
44A ILE* 4.2 15.0 - - + -
48A PRO* 5.7 0.9 - - + -
80A PRO* 4.5 11.7 - - + -
81A GLN 5.4 0.2 - - - -
82A VAL* 3.7 25.6 - - + -
93A VAL* 4.4 6.3 - - + -
94A ILE 3.3 5.2 - - - +
95A VAL* 3.6 28.7 - - + -
134A PHE* 3.5 31.9 - + + -
137A LEU* 6.2 0.2 - - + -
212A LEU* 3.9 33.0 - - + -
213A MET* 1.3 74.6 - - - +
215A THR* 1.3 60.9 + - - +
231A PRO* 3.2 5.0 - - - +
232A VAL* 2.9 41.4 + - - +
234A SER* 4.2 13.9 - - - -
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Residues in contact with THR 215 (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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42A LEU* 5.4 0.4 - - - -
92A LYS 3.7 0.5 - - - +
93A VAL* 3.2 4.6 - - - -
94A ILE* 2.7 51.6 + - - +
96A GLN* 4.4 1.6 + - - -
164A ASN* 3.0 18.6 + - - +
213A MET* 4.0 3.1 + - - +
214A PHE* 1.3 73.5 + - - +
216A ALA* 1.3 67.3 + - - +
217A PHE* 3.5 30.6 - - + -
228A ARG* 3.9 15.9 - - + -
229A LEU 4.3 4.0 - - - +
231A PRO* 2.9 24.5 - - - +
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Residues in contact with ALA 216 (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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42A LEU* 4.0 21.2 - - + +
84A ILE* 3.9 25.4 - - + -
92A LYS 3.1 8.3 - - - +
93A VAL* 4.2 2.9 - - + +
215A THR* 1.3 76.5 - - - +
217A PHE* 1.3 64.1 + - - +
218A LEU* 5.3 0.4 - - + -
228A ARG* 3.7 3.1 - - - -
229A LEU* 3.0 48.2 + - + +
230A GLU 5.8 0.2 + - - -
231A PRO* 5.5 0.2 - - - +
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Residues in contact with PHE 217 (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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91A ALA* 3.5 4.5 - - - -
92A LYS* 2.6 55.9 + - + +
94A ILE* 3.8 21.5 - - + -
162A GLY 4.6 6.3 - - - -
163A TYR* 4.2 24.0 - + - -
164A ASN* 5.1 0.4 - - - -
177A GLN* 6.0 0.4 - - - -
178A ALA* 4.7 12.1 - - + -
215A THR* 3.5 26.7 - - + -
216A ALA* 1.3 74.9 - - - +
218A LEU* 1.3 63.5 + - - +
225A PHE* 3.6 31.8 - - + +
226A THR* 4.0 10.8 - - - -
227A ARG 3.0 6.1 - - - +
228A ARG* 3.7 38.8 - - + -
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Residues in contact with LEU 218 (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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40A PRO* 4.0 19.7 - - + -
84A ILE* 4.5 7.6 - - + -
87A TYR* 3.5 50.9 - - + -
91A ALA* 3.6 13.5 - - + -
217A PHE* 1.3 83.6 - - - +
219A PRO* 1.3 71.7 - - + +
225A PHE* 4.2 2.5 - - - -
226A THR 3.5 2.3 + - - -
227A ARG* 2.7 66.8 + - + +
229A LEU* 4.1 19.1 - - + -
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Residues in contact with PRO 219 (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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87A TYR* 3.3 26.7 - - + +
90A PRO* 3.3 27.1 - - + +
218A LEU* 1.3 83.0 - - + +
220A ASP* 1.3 63.1 + - - +
223A GLY* 3.9 20.4 - - - +
224A SER 3.7 7.6 - - - +
225A PHE* 4.1 14.3 - - + -
227A ARG* 3.1 19.9 + - - +
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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