Contacts of the helix formed by residues 133 - 141 (chain E) in PDB entry 1GUM
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 PHE 133 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 4.5 12.6 - - + -
128E ALA* 2.8 25.2 + - + +
129E ILE 4.5 0.2 - - - -
132E TYR* 1.3 73.8 - - + +
134E PRO* 1.3 72.2 - - + +
136E PHE* 3.3 6.2 + + - -
137E GLU* 2.8 23.7 + - - +
160E LEU* 4.6 6.5 - - + -
163E THR* 5.9 0.2 - - + -
164E ILE* 3.9 33.4 - - + -
167E LEU* 3.9 19.5 - - + -
174E ILE* 3.7 29.6 - - + -
175E LEU* 3.7 22.0 - - + -
178E PHE* 3.6 26.5 - + + -
181E LEU* 3.2 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ALA 3.4 2.9 - - - +
129E ILE 3.0 27.1 - - - +
130E ILE 3.5 14.6 - - - +
131E ARG 4.7 0.7 - - - +
132E TYR 3.1 6.5 - - - +
133E PHE* 1.3 100.2 - - + +
135E VAL* 1.3 63.5 + - + +
137E GLU* 3.9 3.3 - - + +
138E LYS* 3.0 25.1 + - - +
178E PHE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 5.3 0.4 - - + -
131E ARG 3.4 24.0 - - - +
132E TYR 2.8 11.2 + - - +
134E PRO* 1.3 74.8 - - + +
136E PHE* 1.3 67.8 + - + +
138E LYS* 3.5 5.2 + - - +
139E ILE* 3.1 40.8 + - + +
51F LEU* 3.6 46.9 - - + +
52F PHE* 3.7 18.4 - - + -
53F GLN* 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 4.0 31.9 - + + -
99E THR* 3.7 20.6 - - + -
132E TYR* 3.3 36.9 + + + -
133E PHE* 3.9 7.4 - + - +
134E PRO 3.2 0.2 - - - -
135E VAL* 1.3 76.7 - - + +
137E GLU* 1.3 65.4 + - - +
139E ILE* 3.0 18.0 + - + +
140E LEU* 2.9 28.2 + - - +
148E LEU* 4.1 20.0 - - + -
160E LEU* 3.8 32.1 - - + -
181E LEU* 4.0 18.4 - - + -
52F PHE* 4.0 23.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E PHE 2.8 21.3 + - - +
134E PRO* 3.9 4.5 - - + +
136E PHE* 1.3 71.7 - - - +
138E LYS* 1.3 59.4 + - - +
140E LEU* 3.1 2.7 + - - +
141E ARG* 2.7 35.2 + - + +
177E ALA 4.2 1.0 - - - +
178E PHE* 2.8 32.9 - - + +
179E PRO* 2.9 19.8 - - - +
180E PHE* 2.8 42.7 + - + +
181E LEU* 2.7 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PRO 3.0 18.1 + - - +
135E VAL* 3.6 5.8 - - - +
137E GLU* 1.3 76.6 - - - +
139E ILE* 1.3 53.5 + - + +
141E ARG* 3.0 7.3 + - - +
142E GLY* 2.7 34.0 + - - -
48F ASN* 4.6 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 3.4 35.2 - - + +
135E VAL* 3.1 33.7 + - + +
136E PHE* 3.0 19.2 + - + +
138E LYS* 1.3 78.2 - - + +
140E LEU* 1.3 65.5 - - - +
142E GLY* 3.2 8.2 + - - -
143E HIS* 3.3 26.8 + - + +
148E LEU* 3.7 37.0 - - + +
51F LEU* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E PHE 2.9 12.6 + - - +
137E GLU 3.5 6.7 - - - +
139E ILE* 1.3 75.6 - - - +
141E ARG* 1.3 62.4 + - - +
143E HIS* 3.8 11.2 + - + -
144E GLY* 2.9 33.1 + - - -
145E GLN 3.9 18.3 - - - +
147E PHE 4.0 4.0 - - - +
148E LEU* 3.8 23.1 - - + -
180E PHE* 4.2 24.1 - - + +
181E LEU* 4.0 19.7 - - + -
184E TYR* 3.6 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E GLU* 2.7 21.3 + - - +
138E LYS* 3.5 6.1 - - - +
140E LEU* 1.3 79.0 - - - +
142E GLY* 1.3 63.8 + - - +
143E HIS 3.5 0.9 + - - -
144E GLY* 4.2 3.8 + - - -
180E PHE* 3.3 46.1 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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