Contacts of the helix formed by residues 161 - 167 (chain E) in PDB entry 6GL7
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 161 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159E SER 3.8 9.8 + - - +
160E LEU* 1.3 78.1 - - - +
162E PRO* 1.3 79.5 - - + +
163E ARG* 3.1 12.6 + - + +
164E GLU* 3.2 11.9 + - + +
165E LEU* 3.0 23.4 + - - +
252E GLU* 5.4 6.3 + - - +
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Residues in contact with PRO 162 (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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160E LEU 4.6 0.9 - - - +
161E LYS* 1.3 90.5 - - + +
163E ARG* 1.3 57.0 + - - +
165E LEU* 4.0 12.3 - - + -
166E CYS* 2.8 38.8 + - - +
245E VAL* 3.7 21.3 - - + -
252E GLU* 3.3 42.2 - - + +
253E VAL 5.5 0.7 - - - +
254E VAL* 3.7 25.1 - - + -
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Residues in contact with ARG 163 (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* 3.1 8.3 + - + +
162E PRO* 1.3 80.2 - - - +
164E GLU* 1.3 65.5 + - + +
166E CYS* 5.1 0.2 - - - -
167E PHE* 3.2 49.7 + - - +
168E PRO 2.8 23.8 + - - -
169E GLU* 3.5 19.7 + - - +
170E THR 4.4 9.5 + - - -
171E ARG* 4.5 12.9 - - - +
172E PRO* 5.7 1.2 - - - +
254E VAL* 4.2 20.1 - - + +
256E VAL* 3.8 28.3 - - - +
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Residues in contact with GLU 164 (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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39E LYS* 2.8 35.1 + - + +
41E TYR* 5.5 1.6 + - - -
155E PRO* 5.9 0.2 - - - +
160E LEU* 3.9 25.8 - - + +
161E LYS* 3.2 13.5 + - + +
163E ARG* 1.3 86.0 - - + +
165E LEU* 1.3 60.3 + - - +
166E CYS 3.4 0.2 - - - -
167E PHE 4.3 4.3 - - - -
169E GLU* 6.1 4.0 - - - +
190E LEU* 3.1 22.5 - - - +
193E VAL* 3.9 5.4 - - - +
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Residues in contact with LEU 165 (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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160E LEU* 3.6 49.1 - - + +
161E LYS 3.0 23.8 + - - +
162E PRO* 3.8 6.1 - - + +
164E GLU* 1.3 79.6 - - - +
166E CYS* 1.3 59.4 + - - +
189E ARG* 4.8 0.5 + - - -
190E LEU* 4.0 4.1 + - - +
193E VAL* 3.7 41.8 - - + +
197E CYS* 4.7 0.4 - - + -
200E ILE* 3.9 23.1 - - + -
202E VAL* 4.3 14.9 - - + +
204E TYR* 3.6 7.3 + - - -
245E VAL* 3.9 24.0 - - + -
246E HIS* 5.0 4.0 - - + -
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Residues in contact with CYS 166 (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 PRO* 2.8 28.4 + - - +
165E LEU* 1.3 79.1 - - - +
167E PHE* 1.3 69.8 + - + +
188E PHE 3.2 12.0 - - - +
190E LEU* 3.7 5.7 - - - +
202E VAL* 3.5 17.5 - - - -
204E TYR* 2.7 31.1 + - + -
243E CYS* 2.0 48.0 - - - -
244E THR 4.8 0.7 - - - -
245E VAL* 5.0 3.6 - - - -
254E VAL* 4.1 0.7 - - - -
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Residues in contact with PHE 167 (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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163E ARG* 3.2 32.0 + - - +
164E GLU* 4.2 2.8 - - - +
166E CYS* 1.3 85.5 - - + +
168E PRO* 1.3 79.7 - - + +
169E GLU 3.7 0.3 + - - -
172E PRO* 5.7 2.5 - - + -
188E PHE* 4.1 15.0 - + - -
190E LEU* 3.4 13.9 - - - +
204E TYR* 3.9 16.8 - + - -
241E ALA* 3.5 40.8 - - + -
242E VAL 3.8 12.8 - - - -
243E CYS* 3.7 13.0 - - + -
254E VAL* 3.5 26.5 - - + -
256E VAL* 3.5 35.4 - - + -
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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