Contacts of the strand formed by residues 257 - 268 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C ILE* 4.8 2.6 - - - +
164C LEU* 4.7 12.5 + - + +
178C THR 4.8 3.0 + - - -
179C HIS* 3.7 31.5 - + - +
180C ALA* 3.8 15.7 - - + +
199C LEU* 3.8 23.1 - - + -
200C ILE 3.4 8.3 - - - -
201C ASN* 3.5 38.3 - - + +
205C GLU* 3.5 23.8 - - - -
207C VAL* 3.6 31.2 - - + -
252C ARG* 2.7 28.4 + - - -
254C LEU* 3.0 49.0 + - + +
256C ASP* 1.3 89.5 + - + +
258C SER* 1.3 58.9 + - - +
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Residues in contact with SER 258 (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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161C LYS* 3.7 31.3 + - - +
162C ASP 3.2 17.5 - - - -
163C ILE* 4.9 0.7 - - - +
164C LEU* 5.8 0.4 - - - +
199C LEU* 3.4 7.1 - - - -
200C ILE* 2.8 39.5 + - - +
235C LEU* 5.6 0.2 - - - -
252C ARG* 4.1 7.4 - - - -
257C TRP* 1.3 76.8 - - - +
259C ALA* 1.3 63.7 + - - +
261C PRO* 5.5 3.8 - - - +
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Residues in contact with ALA 259 (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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161C LYS* 3.8 1.2 - - - +
162C ASP* 2.9 33.5 + - + +
198C THR 3.2 26.5 - - - +
199C LEU* 4.1 3.1 - - + -
200C ILE* 5.0 2.2 - - - +
235C LEU* 4.1 22.4 - - + -
258C SER* 1.3 77.2 + - - +
260C ASN* 1.3 80.8 + - - +
261C PRO* 3.4 5.4 - - - -
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Residues in contact with ASN 260 (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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160C VAL 3.9 0.3 - - - +
162C ASP* 3.2 18.2 + - - -
194C LEU* 3.8 17.4 - - - +
196C LYS 5.6 1.6 + - - -
198C THR* 4.5 17.2 + - - +
200C ILE* 5.7 0.8 - - - +
235C LEU* 5.2 0.8 - - - +
259C ALA* 1.3 79.8 - - - +
261C PRO* 1.3 74.0 - - - +
262C ARG* 2.6 44.2 + - - +
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Residues in contact with PRO 261 (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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160C VAL 3.4 8.1 - - - +
161C LYS* 4.0 16.6 - - + -
200C ILE* 5.3 11.4 - - + -
258C SER* 5.5 3.6 - - - +
259C ALA* 3.4 5.3 - - - +
260C ASN* 1.3 90.3 - - - +
262C ARG* 1.3 61.2 + - - +
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Residues in contact with ARG 262 (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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101C LEU* 4.6 6.9 - - - +
144C VAL* 4.7 21.7 - - + +
145C GLY* 4.9 9.0 - - - +
159C SER* 3.3 3.6 - - - -
160C VAL* 2.8 64.7 + - + +
161C LYS* 4.2 3.6 - - - +
162C ASP* 3.2 37.5 + - - -
194C LEU* 5.8 0.4 - - - +
237C PRO* 3.9 14.8 - - - +
260C ASN* 2.6 39.3 + - - +
261C PRO* 1.3 75.0 - - - +
263C ASP* 1.3 69.2 + - - +
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Residues in contact with ASP 263 (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 VAL* 3.5 3.1 - - - -
145C GLY* 2.7 34.4 + - - +
146C PRO* 6.0 0.8 - - + +
156C LYS* 4.1 18.7 + - + +
158C GLY 3.7 5.8 - - - +
159C SER* 3.1 21.5 - - - -
262C ARG* 1.3 78.7 - - - +
264C ILE* 1.3 61.2 + - - +
265C TYR* 3.6 30.4 + - + +
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Residues in contact with ILE 264 (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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98C PRO* 5.4 1.6 - - + -
101C LEU* 3.5 16.6 - - + -
105C MET* 3.5 33.9 - - + -
106C MET* 4.8 9.4 - - + -
142C PHE* 5.3 1.1 - - + -
143C ARG 3.6 10.1 - - - +
144C VAL* 3.4 31.6 - - + -
156C LYS* 3.5 5.0 - - - +
157C ILE* 2.9 47.9 + - + -
158C GLY 3.0 13.7 + - - +
159C SER* 4.3 6.1 - - - -
160C VAL* 4.1 11.4 - - + -
262C ARG* 4.9 0.2 - - + -
263C ASP* 1.3 78.3 - - - +
265C TYR* 1.3 66.0 + - - +
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Residues in contact with TYR 265 (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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141C ILE 3.8 0.9 - - - +
142C PHE* 3.2 7.6 - - - +
143C ARG* 2.9 43.1 + - + +
145C GLY 3.3 34.3 - - - -
146C PRO* 4.0 13.8 - - + +
147C GLN* 5.1 3.1 - - - -
154C ALA* 4.1 18.4 - - + -
155C ARG 3.2 6.3 - - - -
156C LYS* 3.8 31.3 - - + +
157C ILE* 4.5 4.0 - - - -
263C ASP* 3.6 35.2 + - + +
264C ILE* 1.3 76.4 - - - +
266C MET* 1.3 59.4 + - - +
267C LEU* 4.1 12.1 - - + -
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Residues in contact with MET 266 (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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140C VAL* 3.7 22.7 - - + -
141C ILE 3.5 3.6 - - - -
142C PHE* 3.5 23.1 - - + -
153C ILE 3.4 2.9 - - - +
154C ALA 3.6 0.2 - - - -
155C ARG* 2.7 55.1 + - + +
157C ILE* 3.9 6.7 - - + +
265C TYR* 1.3 71.7 - - - +
267C LEU* 1.3 61.3 + - - +
268C TYR* 4.6 9.2 - - + -
281C PHE* 4.7 1.1 - - - -
282C ILE* 3.9 30.1 - - + +
285C VAL* 3.7 30.1 - - + -
286C ILE* 3.9 28.0 - - + -
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Residues in contact with LEU 267 (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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140C VAL* 3.5 3.6 - - - +
141C ILE* 2.6 58.2 + - + +
143C ARG* 3.4 33.9 - - + +
147C GLN* 3.9 25.1 - - + +
152C LEU* 3.7 24.5 - - + -
153C ILE 3.0 6.5 - - - +
154C ALA* 3.6 30.3 - - + -
265C TYR* 4.3 9.6 - - + +
266C MET* 1.3 76.5 - - - +
268C TYR* 1.3 66.6 + - - +
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Residues in contact with TYR 268 (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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139C ASP 3.7 18.8 - - - +
140C VAL* 4.5 6.1 - - + -
152C LEU* 3.7 8.7 - - - +
153C ILE* 2.9 55.0 + - + +
155C ARG* 3.2 25.5 + - + -
266C MET* 4.6 17.0 - - + -
267C LEU* 1.3 80.8 - - - +
269C ASN* 1.3 64.8 + - - +
270C HIS* 3.6 36.9 + + + -
274C LEU* 4.2 3.1 - - + -
278C VAL* 5.3 2.5 - - + -
282C ILE* 3.9 46.9 - - + +
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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