Contacts of the strand formed by residues 175 - 180 (chain E) in PDB entry 6C1A
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 SER 175 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLU* 2.7 36.3 + - - -
164E VAL 3.3 12.3 - - - -
165E ILE* 3.9 12.1 - - - -
166E ARG* 5.3 0.2 + - - -
174E LYS* 1.3 79.1 - - - +
176E ASP* 1.3 68.2 + - - +
209E ARG* 2.9 37.8 + - - +
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Residues in contact with ASP 176 (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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162E GLU 4.1 0.7 - - - +
163E GLU* 3.5 2.8 - - - +
164E VAL* 2.9 34.1 + - + +
166E ARG* 2.7 53.1 + - - +
175E SER* 1.3 77.3 - - - +
177E VAL* 1.3 62.6 + - - +
178E TYR* 3.4 28.3 + - + +
310E UNX 3.7 5.6 - - - -
6G T 3.6 12.9 - - + +
5H A 5.0 2.1 + - - +
6H 5CM 4.4 9.4 + - - -
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Residues in contact with VAL 177 (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 19.1 - - + -
162E GLU 3.4 4.7 - - - +
163E GLU* 4.0 18.8 - - + -
176E ASP* 1.3 77.3 - - - +
178E TYR* 1.3 73.3 + - - +
179E TYR* 3.8 14.8 - - + -
188E ARG 4.3 3.5 - - - +
208E PHE* 3.5 45.4 - - + +
209E ARG* 3.7 41.3 - - - +
310E UNX 3.2 10.0 - - - -
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Residues in contact with TYR 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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161E LYS* 3.3 4.5 - - - +
162E GLU* 2.8 38.7 + - + +
164E VAL* 4.0 31.1 - - + +
176E ASP* 3.4 29.2 + - + +
177E VAL* 1.3 82.3 - - - +
179E TYR* 1.3 65.8 + - - +
180E PHE* 4.2 12.6 - - + -
186E LYS* 3.7 28.7 - - + -
187E PHE 3.4 13.0 - - - +
188E ARG* 3.9 39.8 + - + -
308E UNX 4.2 9.0 - - - -
4G A 6.1 0.8 - - + +
5G A 4.5 3.8 + - - -
6G T 3.8 19.1 + - - +
6H 5CM 6.1 1.3 - - + -
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Residues in contact with TYR 179 (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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152E CYS* 3.9 6.7 - - - -
155E LEU* 3.5 30.5 - - + -
159E TRP* 4.3 14.4 - - + -
160E LYS 3.2 20.4 - - - +
161E LYS* 3.5 22.8 - - + +
177E VAL* 3.8 7.6 - - + -
178E TYR* 1.3 73.3 - - - +
180E PHE* 1.3 66.1 + - - +
185E LYS 3.6 0.5 - - - +
186E LYS* 3.4 4.3 - - - +
187E PHE* 2.8 41.3 + - + +
193E LEU* 4.5 5.4 - - + -
206E PHE* 3.5 10.7 - + - -
208E PHE* 2.6 65.0 + + - -
211E GLY* 3.1 22.0 + - - -
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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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149E ARG* 3.2 57.7 - - + +
158E GLY 4.0 0.3 - - - +
159E TRP* 3.3 9.9 - - - -
160E LYS* 2.9 47.8 + - + +
162E GLU* 3.6 37.9 - - + -
178E TYR* 4.2 12.6 - - + -
179E TYR* 1.3 78.6 - - - +
181E SER* 1.3 68.8 + - - +
184E GLY* 3.9 16.2 - - - -
185E LYS 3.3 4.3 - - - +
186E LYS* 3.6 39.0 - - + -
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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