Contacts of the helix formed by residues 177 - 181 (chain E) in PDB entry 1U1C
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 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B GLU* 3.8 5.4 - - - +
190B MET* 3.8 17.5 - - + -
164E PRO* 5.1 0.2 - - - +
175E ARG* 3.8 9.5 - - - +
176E VAL* 1.3 73.3 - - + +
178E ARG* 1.3 68.9 + - + +
179E HIS* 4.1 10.1 - - + +
180E PHE* 2.9 30.5 + - + -
181E LYS 3.1 9.2 + - - -
121F LEU 3.8 9.0 - - - +
122F HIS 3.4 28.3 + - - +
123F PHE 3.5 29.2 - - - +
124F ALA* 4.0 6.1 - - - -
125F PRO* 4.0 9.0 - - + -
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Residues in contact with ARG 178 (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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178B ARG* 3.4 18.0 + - - +
179B HIS* 3.5 21.1 + - - +
181B LYS* 2.8 29.2 + - - +
182B GLY 3.6 4.6 + - - -
183B SER* 3.5 23.8 - - - +
186B GLU* 3.5 28.3 + - + +
178C ARG* 4.1 7.0 + - - +
176E VAL 3.6 1.6 + - - -
177E VAL* 1.3 75.4 - - + +
179E HIS* 1.3 65.1 + - - +
181E LYS* 3.1 28.9 + - + +
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Residues in contact with HIS 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ARG* 3.7 20.0 + - - +
127D GLU* 4.3 17.4 + - - -
116E LEU* 5.9 1.2 - - - +
177E VAL* 3.1 13.7 + - + +
178E ARG* 1.3 81.1 - - - +
180E PHE* 1.3 90.2 + + + +
183E SER* 4.6 1.2 - - - -
121F LEU* 5.1 4.9 - - + +
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Residues in contact with PHE 180 (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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116E LEU* 4.0 36.3 - - + -
164E PRO 3.6 15.0 - - - +
165E GLY* 3.9 16.8 - - - -
167E GLU* 3.3 11.8 - - - +
176E VAL* 3.6 10.5 - - + -
177E VAL* 2.9 19.3 + - + +
179E HIS* 1.3 100.8 - + - +
181E LYS* 1.3 62.5 + - - +
183E SER* 2.8 39.2 + - - +
187E TRP* 5.5 1.3 - + - -
121F LEU* 4.3 4.0 - - + -
122F HIS* 3.4 52.7 - + + -
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Residues in contact with LYS 181 (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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178C ARG* 2.8 35.1 + - - +
167E GLU* 4.1 2.5 - - - -
169E TYR* 3.4 27.1 + - + +
176E VAL* 3.3 28.3 - - + +
177E VAL 3.1 6.5 + - - +
178E ARG* 3.1 19.1 + - + +
180E PHE* 1.3 75.4 - - - +
182E GLY* 1.3 55.5 + - - +
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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
------------------------------------------------------------
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