Contacts of the helix formed by residues 130 - 143 (chain A) in PDB entry 5E6J
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 ALA 130 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR 4.1 3.6 - - - +
73A TYR 4.0 1.1 - - - +
74A HIS* 3.6 23.7 - - + -
128A PHE* 3.4 2.1 - - - +
129A ASN* 1.3 78.5 - - - +
131A PRO* 1.3 71.0 - - + +
132A ALA 3.2 0.7 - - - -
133A LEU* 2.9 18.5 + - + +
134A GLN* 2.9 21.0 + - - +
155A TYR* 3.8 22.0 - - - +
176A HIS* 4.1 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.4 24.2 - - + +
72A TYR* 3.4 26.5 - - + +
74A HIS* 4.1 5.4 - - + -
129A ASN 3.4 9.6 - - - +
130A ALA* 1.3 81.7 - - - +
132A ALA* 1.3 56.9 + - - +
134A GLN* 3.3 5.6 + - + +
135A GLU* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.5 51.9 + - + +
73A TYR* 4.2 11.4 - - + -
84A TYR* 5.8 1.1 - - + +
130A ALA 3.2 0.6 - - - -
131A PRO* 1.3 79.3 - - - +
133A LEU* 1.3 58.5 + - - +
135A GLU* 3.7 4.0 - - - +
136A ALA* 2.9 32.2 + - - +
151A LEU* 3.8 15.6 - - + +
155A TYR* 4.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.3 39.7 - - + -
130A ALA* 2.9 17.7 + - + +
132A ALA* 1.3 80.0 - - - +
134A GLN* 1.3 57.7 + - - +
136A ALA* 3.7 0.3 - - - +
137A TYR* 2.8 31.2 + - - +
148A PHE* 3.6 30.5 - - + +
151A LEU* 4.0 14.6 - - + +
152A ILE* 5.3 2.2 - - + +
155A TYR* 4.1 30.0 + - + +
173A LEU* 4.7 11.2 - - + +
176A HIS* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL 5.0 2.0 + - - -
127A LYS* 3.4 24.5 - - - +
128A PHE* 2.7 48.7 + - - +
130A ALA 2.9 7.8 + - - +
131A PRO* 3.7 9.9 - - + +
133A LEU* 1.3 74.0 - - - +
135A GLU* 1.3 60.6 + - - +
137A TYR* 3.1 29.5 + - - +
138A TYR* 2.9 61.4 + - + +
135D GLU* 4.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 5.3 7.9 + - - -
72A TYR* 4.6 15.1 + - + -
131A PRO 2.9 17.2 + - - +
132A ALA* 3.7 4.6 - - - +
134A GLN* 1.3 75.1 - - - +
136A ALA* 1.3 60.5 + - - +
138A TYR* 3.2 11.9 + - - +
139A ARG* 2.9 53.4 + - - +
127D LYS* 4.7 9.8 + - - -
134D GLN* 6.0 1.0 - - - +
138D TYR* 3.5 35.5 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
84A TYR* 5.5 0.2 - - - +
132A ALA 2.9 18.3 + - - +
133A LEU 3.8 2.7 - - - +
135A GLU* 1.3 77.7 + - - +
137A TYR* 1.3 51.8 + - - +
139A ARG* 3.6 12.1 - - - +
140A ALA* 2.7 34.7 + - - +
144A ASP 4.2 0.9 - - - +
147A ASN* 4.2 8.5 - - + -
148A PHE* 3.7 32.9 - - + +
151A LEU* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 5.3 1.3 - - + -
121A LEU* 2.5 47.0 + - + -
122A GLN* 3.5 10.6 - - + -
124A LEU 3.9 7.0 + - - -
126A VAL* 4.3 19.8 - - + +
128A PHE* 3.8 18.2 - + + -
133A LEU 2.8 18.8 + - - +
134A GLN* 3.3 24.0 - - - +
136A ALA* 1.3 73.8 - - - +
138A TYR* 1.3 62.7 + + - +
140A ALA* 3.0 6.9 + - + +
141A ARG* 2.8 67.9 + - + +
148A PHE* 3.5 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 4.5 13.0 + - - +
134A GLN* 2.9 54.1 + - + +
135A GLU* 3.6 9.2 - - - +
137A TYR* 1.3 74.7 - + - +
139A ARG* 1.3 59.8 + - - +
141A ARG* 3.1 24.8 + - - +
142A ALA* 2.9 28.8 + - - +
135D GLU* 3.9 25.9 + - + -
138D TYR* 4.0 26.0 - + + +
139D ARG* 3.5 47.4 + - + -
142D ALA* 4.4 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 6.1 1.4 - - - +
135A GLU* 2.9 39.8 + - - +
136A ALA* 3.6 8.7 - - - +
138A TYR* 1.3 75.8 - - - +
140A ALA* 1.3 57.0 + - - +
142A ALA* 3.3 9.7 + - - +
143A GLY 3.0 9.0 + - - -
144A ASP* 2.8 61.1 + - + +
147A ASN* 2.9 30.3 + - + +
138D TYR* 3.8 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 3.1 19.3 + - - +
118A LEU* 4.0 15.5 - - + -
122A GLN* 5.3 0.9 - - - -
136A ALA 2.7 18.5 + - - +
137A TYR* 3.0 11.9 + - + +
139A ARG* 1.3 71.2 - - - +
141A ARG* 1.3 65.8 + - - +
143A GLY* 3.0 12.5 + - - -
144A ASP 3.1 7.8 + - - -
145A ALA* 3.5 24.5 - - + -
148A PHE* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 4.3 2.9 + - - +
103A THR* 3.6 10.5 + - - -
122A GLN* 3.2 41.7 + - + +
124A LEU 5.0 6.6 + - - -
126A VAL 5.8 0.8 + - - -
137A TYR* 2.8 62.3 + - + +
138A TYR* 3.1 23.5 + - - +
140A ALA* 1.3 72.3 - - - +
142A ALA* 1.3 63.5 + - - +
142D ALA* 4.0 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 3.5 8.8 + - - -
138A TYR 2.9 12.7 + - - +
139A ARG* 3.3 14.4 - - - +
141A ARG* 1.3 78.3 - - - +
143A GLY* 1.3 55.3 + - - +
144A ASP* 3.9 1.6 - - + +
138D TYR* 4.7 3.4 - - + +
141D ARG* 4.0 43.9 - - + +
142D ALA* 4.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.6 24.5 - - - +
98A GLN* 3.5 16.8 - - - -
103A THR* 4.1 2.9 - - - -
139A ARG 3.0 0.4 + - - -
140A ALA 3.0 13.3 + - - -
142A ALA* 1.3 78.7 - - - +
144A ASP* 1.3 60.6 + - - +
145A ALA 3.6 4.4 + - - -
----------------------------------------------------------
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