Contacts of the strand formed by residues 176 - 184 (chain A) 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 LYS 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 2.6 27.7 + - - -
169A PRO 3.2 19.4 + - - -
170A ASN* 3.3 33.7 - - + +
172A ASP* 4.5 9.0 - - - -
174A PHE* 4.1 4.7 - - + -
175A ASP* 1.3 76.5 - - - +
177A LEU* 1.3 60.5 + - - +
178A TYR* 3.0 28.6 + - + +
235A THR 3.8 0.3 - - - +
236A ILE* 3.3 4.5 - - - -
237A VAL* 2.8 35.7 + - + +
257A TYR* 3.5 44.4 - - + -
258A PHE 3.8 4.9 - - - -
260A MET* 4.8 0.4 - - - -
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Residues in contact with LEU 177 (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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70A LEU* 4.7 6.5 - - + -
111A LEU* 4.0 12.6 - - + -
112A VAL* 4.8 8.5 - - + -
176A LYS* 1.3 71.5 - - - +
178A TYR* 1.3 61.9 + - - +
179A ILE* 3.9 15.5 - - + -
234A TRP* 3.9 27.6 - - + -
235A THR 3.6 3.1 - - - +
236A ILE* 3.9 18.2 - - + +
257A TYR* 3.6 2.1 - - - -
258A PHE* 2.9 61.4 + - + +
260A MET* 3.7 33.8 - - + +
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Residues in contact with TYR 178 (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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123A GLU* 2.8 29.4 + - - -
125A PHE* 3.9 7.9 - + - -
168A MET* 3.5 12.6 + - + +
176A LYS* 3.0 38.2 + - + +
177A LEU* 1.3 75.3 - - - +
179A ILE* 1.3 61.1 + - - +
180A TRP* 3.8 9.7 - - + -
234A TRP* 3.3 5.0 - - - +
235A THR* 2.8 40.2 + - - +
237A VAL* 3.6 34.4 - - + +
243A LEU* 3.7 30.1 - - + -
254A PRO* 4.2 15.5 - - + -
256A GLY 3.2 27.8 - - - -
257A TYR* 4.0 2.2 - - + -
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Residues in contact with ILE 179 (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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70A LEU* 3.9 9.9 - - + -
71A LEU* 3.6 19.7 - - + -
108A LEU* 3.7 22.9 - - + -
150A ARG* 5.0 1.9 - - + +
151A LEU* 3.6 15.0 - - + +
177A LEU* 3.9 11.6 + - + -
178A TYR* 1.3 71.7 - - - +
180A TRP* 1.3 65.0 + - - +
232A ILE* 3.6 25.4 - - + -
233A TYR 3.4 2.0 - - - +
234A TRP* 3.6 26.2 - - + -
254A PRO* 3.4 19.1 - - - +
256A GLY 5.1 1.2 + - - -
258A PHE* 3.8 31.8 - - + -
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Residues in contact with TRP 180 (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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151A LEU* 4.1 9.4 - - - -
178A TYR* 3.8 20.4 - - + -
179A ILE* 1.3 74.9 - - - +
181A GLY* 1.3 82.5 + - - +
182A ILE* 5.2 0.4 - - + -
202A VAL* 3.8 22.0 - - + -
204A VAL* 3.5 39.4 - - + +
211A GLN* 3.7 19.7 - - + -
213A ILE* 3.4 30.7 - - + -
232A ILE* 3.6 8.5 - - - +
233A TYR* 2.8 56.4 + + + +
234A TRP 4.1 1.4 - - - -
235A THR* 2.9 23.7 + - - +
243A LEU* 6.0 0.4 - - + -
245A ILE* 6.1 1.1 - - + -
251A LEU* 4.9 3.1 - - + -
252A ILE 3.8 12.3 - - - +
254A PRO* 3.9 17.7 - - + -
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Residues in contact with GLY 181 (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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180A TRP* 1.3 91.0 - - - +
182A ILE* 1.3 61.0 + - - +
202A VAL* 4.6 0.5 - - - +
230A ILE* 5.9 0.4 - - - -
231A SER 3.1 15.0 - - - -
232A ILE* 4.4 3.4 - - - -
233A TYR* 4.4 1.6 - - - -
251A LEU* 3.7 9.4 - - - +
252A ILE* 3.0 37.5 + - - +
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Residues in contact with ILE 182 (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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180A TRP* 5.3 0.7 - - + -
181A GLY* 1.3 74.2 - - - +
183A HIS* 1.3 63.6 + - - +
184A HIS* 4.0 18.7 + - + +
201A ARG 4.9 0.2 - - - -
202A VAL* 3.7 17.7 - - + +
213A ILE* 3.5 49.8 - - + +
215A PRO* 3.5 27.6 - - + -
230A ILE* 3.3 4.3 - - - +
231A SER* 3.1 23.3 + - - +
233A TYR* 4.1 13.2 - - + -
250A ASN* 3.2 21.1 - - + +
252A ILE* 4.1 4.6 - - - +
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Residues in contact with HIS 183 (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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98A TYR* 2.8 29.7 + + - -
153A TRP* 3.7 11.6 - + - -
182A ILE* 1.3 72.2 - - - +
184A HIS* 1.3 59.5 + - - +
185A PRO* 3.6 13.4 - - + +
190A GLU* 3.3 23.0 + - - -
194A LEU* 3.8 14.4 - - + -
195A TYR* 2.8 35.7 + - + +
215A PRO* 3.4 7.7 - - - +
228A SER* 4.0 2.0 - - - -
229A ARG 4.0 4.0 - - - -
230A ILE* 3.8 23.6 - - + -
250A ASN* 2.8 38.6 + - - +
252A ILE* 4.1 8.0 - - + +
329A SIA 3.7 4.2 - - - -
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Residues in contact with HIS 184 (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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182A ILE* 4.1 13.8 - - + +
183A HIS* 1.3 73.3 - - - +
185A PRO* 1.3 65.8 - - - +
213A ILE* 5.2 2.5 - - + -
214A ILE 4.3 2.7 - - - -
215A PRO* 3.3 12.9 - - + +
216A ASN* 2.7 56.0 + - - +
220A ARG* 3.3 11.4 + - - +
228A SER* 3.3 20.4 - - - -
229A ARG 2.9 24.5 + - - +
231A SER* 2.8 33.6 + - - -
233A TYR* 5.9 0.7 - - - -
210C GLN* 3.6 19.1 + - - -
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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