Contacts of the helix formed by residues 131 - 142 (chain A) in PDB entry 5GKI
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 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.2 20.4 + - - +
129A THR* 4.7 0.5 - - - -
130A GLY* 1.3 77.6 + - - +
132A GLU* 1.3 65.5 + - - +
133A ALA* 4.0 8.3 + - - +
134A GLU* 3.2 27.9 + - - +
135A MET* 3.2 22.5 + - - +
182A ARG* 4.1 12.6 - - - +
237A PRO* 4.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 1.3 74.6 - - - +
133A ALA* 1.3 64.4 + - - +
135A MET* 3.1 21.1 + - - +
136A ALA* 3.1 11.3 + - + +
156A GLU* 4.7 11.1 - - - +
165A ALA* 4.0 10.2 - - - +
180A LEU* 3.0 46.7 - - + +
181A LYS* 3.8 11.7 + - - +
182A ARG* 4.3 17.7 + - + +
301A MG 3.9 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.2 7.7 - - - +
132A GLU* 1.3 81.0 - - - +
134A GLU* 1.3 59.1 + - + +
136A ALA* 3.2 11.0 + - - +
137A GLU* 3.0 38.8 + - - +
155A ARG* 5.6 0.2 - - - -
102C MPD 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 4.1 5.1 - - - +
129A THR* 2.3 39.3 + - - -
130A GLY 2.9 12.6 + - - -
131A SER* 3.2 22.6 + - - +
132A GLU 3.2 0.4 - - - -
133A ALA* 1.3 76.9 - - + +
135A MET* 1.3 64.4 + - - +
137A GLU* 3.6 16.1 + - - +
138A LEU* 3.0 22.3 + - - +
238A PRO* 3.2 21.9 - - + +
240A ARG* 3.7 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER 3.2 12.4 + - - +
132A GLU* 3.1 10.6 + - - +
134A GLU* 1.3 75.5 - - - +
136A ALA* 1.3 65.2 + - - +
138A LEU* 3.1 8.2 + - - +
139A ILE* 3.0 26.0 + - + +
180A LEU* 4.2 16.2 - - + -
181A LYS 3.6 25.4 - - - +
182A ARG* 3.8 15.7 - - - -
213A VAL* 4.0 17.5 - - + +
235A LEU* 3.8 47.0 - - + +
236A GLU 4.9 0.2 - - - +
237A PRO* 3.7 22.0 - - + -
238A PRO* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.1 9.5 + - + +
133A ALA* 3.2 12.6 - - - +
135A MET* 1.3 79.0 - - - +
137A GLU* 1.3 58.8 + - - +
139A ILE* 2.9 23.5 + - - +
140A PHE* 2.9 18.6 + - - -
155A ARG* 4.0 26.5 - - + -
166A VAL* 4.6 8.1 - - + -
180A LEU* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA* 3.0 27.3 + - - +
134A GLU* 3.8 17.2 - - - +
135A MET 3.3 0.2 - - - -
136A ALA* 1.3 72.4 - - + +
138A LEU* 1.3 66.6 + - - +
140A PHE* 3.1 7.5 + - - +
141A GLU* 2.9 35.6 + - - +
155A ARG* 4.8 13.7 - - - +
240A ARG* 4.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU 3.0 14.3 + - - +
135A MET 3.2 10.3 - - - +
137A GLU* 1.3 75.6 - - - +
139A ILE* 1.3 54.1 + - - +
141A GLU* 3.3 7.9 + - + +
142A ASN* 2.7 56.2 + - + +
145A VAL* 4.2 17.9 - - + -
235A LEU* 4.5 18.8 - - + -
236A GLU 4.7 4.5 - - - +
238A PRO* 4.0 29.6 - - + -
240A ARG* 4.5 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A MET* 3.0 16.1 + - + +
136A ALA* 2.9 10.1 + - - +
138A LEU* 1.3 77.1 - - - +
140A PHE* 1.3 58.8 + - + +
142A ASN 4.2 6.1 - - - -
143A PRO* 3.0 28.2 - - + +
145A VAL* 4.0 14.6 - - + -
146A ILE* 3.8 35.9 - - + -
150A PHE* 4.1 16.4 - - + -
152A PRO* 4.2 2.8 - - + +
166A VAL* 4.7 9.0 - - + -
178A LEU* 3.8 16.8 - - + -
180A LEU* 3.9 24.9 - - + -
213A VAL* 4.7 4.7 - - + -
235A LEU* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA 2.9 18.5 + - - +
137A GLU* 3.1 6.2 + - - +
139A ILE* 1.3 80.8 - - + +
141A GLU* 1.3 61.0 + - - +
142A ASN 3.3 0.3 + - - -
143A PRO* 3.3 13.0 - - - +
152A PRO* 3.7 37.1 - - + +
153A LEU 4.0 14.8 - - - -
154A PHE 3.8 25.1 - - - -
155A ARG* 3.8 44.6 - - + +
166A VAL* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 2.9 25.6 + - - +
138A LEU* 3.6 9.6 - - + +
140A PHE* 1.3 76.1 - - - +
142A ASN* 1.3 75.6 + - - +
143A PRO* 3.7 3.3 - - - +
240A ARG* 3.2 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 2.7 25.4 + - + +
139A ILE 3.3 3.6 - - - -
141A GLU* 1.3 95.2 + - - +
143A PRO* 1.3 67.1 - - - +
144A GLU* 2.7 32.3 + - - +
145A VAL* 3.0 33.4 + - + +
----------------------------------------------------------
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