Contacts of the strand formed by residues 257 - 269 (chain E) in PDB entry 5FHK
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 TRP 257 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162E ASP 4.8 0.3 - - - +
163E ILE* 4.8 3.3 - - - +
164E LEU* 4.7 10.9 + - + +
178E THR 4.8 4.2 + - - -
179E HIS* 5.0 6.3 - + + -
180E ALA* 3.8 23.5 - - + +
181E GLU* 5.5 1.1 - - - -
199E LEU* 3.6 28.7 - - + -
200E ILE 3.5 7.0 - - - -
201E ASN* 3.4 42.6 - - + +
205E GLU* 3.6 25.6 - - + -
207E VAL* 3.7 28.3 - - + -
252E ARG* 3.0 21.4 + - - -
254E LEU* 2.8 47.8 + - + +
255E PRO 3.2 0.2 - - - -
256E ASP* 1.3 93.2 - - + +
258E SER* 1.3 62.1 + - - +
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Residues in contact with SER 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LYS* 3.7 35.2 + - - +
162E ASP 3.3 14.8 - - - -
163E ILE* 5.0 0.4 - - - +
164E LEU 6.0 0.2 - - - +
199E LEU* 3.5 8.7 - - - -
200E ILE* 2.8 43.5 + - - +
252E ARG* 4.3 2.0 - - - -
256E ASP 4.4 0.2 + - - -
257E TRP* 1.3 77.2 - - - +
259E ALA* 1.3 63.5 + - - +
261E PRO* 5.4 3.6 - - - +
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LYS* 3.8 2.1 - - - +
162E ASP* 2.9 31.3 + - + +
198E THR 3.2 25.6 - - - +
199E LEU* 4.3 1.8 - - + -
200E ILE* 4.7 1.8 - - - -
235E LEU* 4.0 23.3 - - + -
258E SER* 1.3 74.8 - - - +
260E ASN* 1.3 83.8 + - - +
261E PRO* 3.3 6.3 - - - -
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Residues in contact with ASN 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E VAL 4.0 0.2 - - - +
162E ASP* 2.8 21.8 + - - -
194E LEU* 3.5 17.9 - - - +
196E LYS 5.5 0.8 + - - -
198E THR* 4.4 16.8 + - - +
200E ILE* 5.4 1.0 - - - +
235E LEU* 4.6 0.8 - - - +
259E ALA* 1.3 84.5 - - - +
261E PRO* 1.3 74.0 - - - +
262E ARG* 2.7 44.4 + - - +
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Residues in contact with PRO 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E VAL 3.5 8.7 - - - +
161E LYS* 3.9 16.2 - - + -
200E ILE* 5.1 11.9 - - + -
258E SER* 5.4 3.1 - - - +
259E ALA* 3.3 4.6 - - - -
260E ASN* 1.3 88.4 - - - +
262E ARG* 1.3 58.7 + - - +
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Residues in contact with ARG 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 4.4 8.1 - - - +
144E VAL* 3.6 36.9 - - + +
145E GLY* 5.0 3.4 - - - +
159E SER* 3.3 5.1 - - - -
160E VAL* 3.0 57.8 + - + +
161E LYS* 4.0 3.6 - - - +
162E ASP* 3.1 35.8 + - - -
194E LEU* 6.0 0.2 - - - +
237E PRO* 3.9 16.8 - - - +
260E ASN* 2.7 38.6 + - - +
261E PRO* 1.3 74.4 - - - +
263E ASP* 1.3 64.4 + - - +
264E ILE* 4.6 2.0 - - + -
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Residues in contact with ASP 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLY* 3.1 27.2 + - - +
156E LYS* 2.4 45.6 + - + +
158E GLY 3.4 6.7 - - - +
159E SER* 3.4 12.6 - - - -
262E ARG* 1.3 76.4 - - - +
264E ILE* 1.3 67.2 + - - +
265E TYR* 3.7 25.7 + - + -
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Residues in contact with ILE 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E PRO* 4.9 2.0 - - + -
101E LEU* 4.0 4.5 - - + -
105E MET* 3.5 37.9 - - + -
106E MET* 4.9 3.4 - - - -
142E PHE* 5.0 4.9 - - + -
143E ARG 3.5 7.0 - - - +
144E VAL* 3.6 28.5 - - + -
156E LYS* 3.5 3.7 - - - -
157E ILE* 2.8 57.2 + - + +
158E GLY 3.0 14.1 + - - +
159E SER* 4.9 0.2 - - - -
160E VAL* 4.0 27.8 - - + +
262E ARG* 4.6 2.0 - - + +
263E ASP* 1.3 78.6 - - - +
265E TYR* 1.3 60.0 - - - +
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Residues in contact with TYR 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ILE 3.7 0.9 - - - +
142E PHE* 3.2 6.1 - - - +
143E ARG* 2.9 35.4 + - + +
145E GLY* 3.3 38.8 - - - +
146E PRO* 3.8 19.7 - - + +
154E ALA* 4.2 15.7 - - + -
155E ARG* 3.3 6.5 - - - +
156E LYS* 3.8 32.0 - - + +
157E ILE* 4.8 1.1 - - - -
263E ASP* 3.7 37.6 + - + +
264E ILE* 1.3 76.8 - - - +
266E MET* 1.3 59.4 + - - +
267E LEU* 4.1 16.8 - - + -
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Residues in contact with MET 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 3.7 22.7 - - + -
141E ILE 3.4 3.6 - - - -
142E PHE* 3.6 19.7 - - + -
153E ILE 3.6 1.7 - - - +
154E ALA* 3.5 2.6 - - - -
155E ARG* 2.8 51.3 + - + +
157E ILE* 4.1 13.2 - - + +
265E TYR* 1.3 73.6 - - - +
267E LEU* 1.3 63.3 - - - +
268E TYR* 4.8 7.5 - - + -
282E ILE* 4.2 27.1 - - + -
285E VAL* 3.7 37.9 - - + -
286E ILE* 4.3 14.8 - - + -
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Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 3.4 5.5 - - - +
141E ILE* 2.6 56.4 + - + +
143E ARG* 3.7 32.1 - - + -
147E GLN* 5.4 10.1 - - + +
152E LEU* 4.2 28.9 - - + -
153E ILE 3.4 5.2 - - - +
154E ALA* 3.5 31.2 - - + -
265E TYR* 4.1 11.4 - - + -
266E MET* 1.3 78.3 - - - +
268E TYR* 1.3 66.3 + - - +
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Residues in contact with TYR 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ASP 3.8 15.0 - - - +
140E VAL* 4.4 1.3 - - + -
152E LEU* 3.4 8.2 - - - -
153E ILE* 3.0 70.0 + - + +
155E ARG* 5.9 4.0 - - + -
266E MET* 4.8 13.0 - - + -
267E LEU* 1.3 79.5 - - - +
269E ASN* 1.3 64.1 + - - +
270E HIS* 4.1 9.6 - - + +
274E LEU* 3.5 33.2 - - + -
282E ILE* 3.4 43.5 - - + +
286E ILE* 6.0 1.5 - - + +
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Residues in contact with ASN 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PRO* 6.0 3.5 - - + +
136E THR* 5.9 4.6 - - - +
138E TRP 6.2 0.2 - - - +
139E ASP 4.8 2.4 + - - -
151E SER* 3.5 28.3 + - - -
152E LEU* 3.7 11.8 - - + +
268E TYR* 1.3 74.6 - - - +
270E HIS* 1.3 59.2 + - - +
271E LYS* 2.9 6.1 + - - +
272E ASP* 2.7 55.5 + - + +
274E LEU* 3.3 26.1 - - + +
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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