Contacts of the strand formed by residues 251 - 259 (chain C) in PDB entry 5HMG
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 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C TRP* 4.0 14.8 - - + -
153C TRP* 4.3 0.5 - - - -
154C LEU* 3.7 33.4 + - + +
161C TYR* 3.8 10.2 + - - +
164C LEU* 4.3 6.5 - - + -
180C TRP* 4.9 6.7 - - + -
181C GLY 3.7 8.3 - - - +
195C TYR* 5.1 0.2 - - - -
202C VAL* 3.8 21.5 - - + -
245C ILE* 3.9 24.7 - - + -
247C SER* 3.7 24.5 - - - +
249C GLY 3.2 3.8 + - - -
250C ASN* 1.3 77.6 - - - +
252C ILE* 1.3 83.8 + - - +
253C ALA* 3.7 24.9 + - + +
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Residues in contact with ILE 252 (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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147C PHE* 4.0 15.0 - - + -
151C LEU* 3.8 41.7 - - + -
152C ASN 3.7 3.6 - - - +
153C TRP* 3.4 42.2 - - + +
180C TRP* 3.8 2.6 - - - +
181C GLY* 3.0 45.2 + - - +
182C ILE 4.1 13.2 - - - +
183C HIS* 4.1 9.2 - - + +
230C ILE* 4.3 13.0 - - + -
232C ILE* 5.8 0.2 - - + -
251C LEU* 1.3 77.0 - - - +
253C ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 253 (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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127C TRP* 3.5 33.7 - - + -
151C LEU* 3.5 5.9 - - - +
152C ASN* 2.7 52.2 + - + +
154C LEU* 4.2 5.8 - - + +
251C LEU* 3.7 17.7 - - + -
252C ILE* 1.3 72.7 - - - +
254C PRO* 1.3 68.6 - - + +
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Residues in contact with PRO 254 (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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125C PHE* 3.6 19.8 - - + +
127C TRP* 4.6 2.0 + - + -
150C ARG 4.3 2.5 - - - +
152C ASN* 4.9 1.4 - - - +
178C TYR* 4.2 18.4 - - + -
179C ILE 3.4 24.7 - - - +
180C TRP* 3.9 17.0 - - + -
245C ILE* 3.5 31.6 - - + -
251C LEU* 5.0 1.6 - - + -
253C ALA* 1.3 92.2 - - + +
255C ARG* 1.3 60.8 + - - +
256C GLY 3.6 15.8 + - - +
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Residues in contact with ARG 255 (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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120C PHE* 3.5 13.8 - - + -
122C THR* 3.2 18.5 - - + +
123C GLU 2.9 20.0 + - - +
125C PHE* 4.3 5.8 - - - -
132C GLN* 4.4 3.0 - - - +
133C ASN* 2.7 44.1 + - - +
147C PHE* 5.9 2.0 - - - +
148C PHE 4.7 2.6 + - - -
149C SER* 3.3 24.3 + - - +
150C ARG 3.3 21.7 + - - +
151C LEU 2.6 33.6 + - - -
152C ASN* 3.4 26.5 + - + +
153C TRP 5.2 0.2 - - - +
254C PRO* 1.3 73.0 - - - +
256C GLY* 1.3 54.2 + - - +
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Residues in contact with GLY 256 (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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120C PHE* 3.3 11.6 - - - -
121C ILE 3.2 11.7 - - - -
123C GLU* 3.6 19.3 - - - -
125C PHE* 4.0 4.0 - - - -
178C TYR* 3.2 22.6 - - - -
179C ILE 5.0 1.0 + - - -
254C PRO* 3.3 9.4 + - - +
255C ARG* 1.3 77.7 + - - +
257C TYR* 1.3 60.1 + - - -
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Residues in contact with TYR 257 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C GLU 3.8 0.2 - - - +
120C PHE* 3.2 8.9 - - - -
121C ILE* 2.9 74.5 + - + +
123C GLU* 3.5 27.1 - - + -
172C ASP* 3.8 7.8 + - - -
174C PHE* 3.3 39.3 - + - -
176C LYS* 3.5 41.1 - - + -
177C LEU 3.6 10.8 - - - +
178C TYR* 3.9 8.7 - - + -
256C GLY* 1.3 74.6 - - - +
258C PHE* 1.3 72.9 + - - +
259C LYS* 4.1 4.7 - - + -
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Residues in contact with PHE 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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70C LEU* 3.4 48.9 - - + -
117C THR 5.4 1.8 - - - +
118C LEU* 3.7 38.4 - - + -
119C GLU 3.4 3.1 - - - +
120C PHE* 3.9 22.9 - + + -
150C ARG* 3.8 21.1 - - + -
176C LYS* 3.8 0.7 - - - -
177C LEU* 3.0 63.8 + - + +
179C ILE* 3.8 20.0 - - + -
257C TYR* 1.3 81.4 - - - +
259C LYS* 1.3 65.4 + - - +
260C MET* 3.7 0.4 + - + -
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Residues in contact with LYS 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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115C SER* 3.5 2.1 + - - -
117C THR* 3.1 21.7 - - - +
119C GLU* 3.2 39.6 + - + +
121C ILE* 4.5 11.2 - - + -
174C PHE* 3.2 51.7 - - - +
175C ASP 4.5 2.0 - - - -
257C TYR* 4.0 18.3 + - + -
258C PHE* 1.3 75.9 - - - +
260C MET* 1.3 69.1 + - - +
261C ARG* 3.8 21.7 - - - +
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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