Contacts of the helix formed by residues 128 - 138 (chain A) in PDB entry 1SXG
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 THR 128 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 3.1 23.5 + - - +
126A ASN* 3.0 33.5 + - + +
127A VAL* 1.3 72.9 - - - +
129A GLU* 1.3 68.5 + - - +
130A GLU* 3.1 12.9 + - - +
131A HIS* 2.9 41.8 + - - +
132A VAL* 3.1 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL 4.6 4.3 - - - +
128A THR* 1.3 82.6 - - - +
130A GLU* 1.3 61.2 + - - +
132A VAL* 3.4 12.7 - - + +
133A GLU* 3.0 33.3 + - - +
149A GLU* 5.2 1.2 - - - +
150A SER* 5.8 3.5 - - - -
151A THR* 4.5 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 2.7 29.7 + - - +
106A LEU* 3.6 20.9 - - + +
128A THR* 3.0 8.2 + - - +
129A GLU* 1.3 76.1 - - - +
131A HIS* 1.3 68.6 + - - +
133A GLU* 3.0 18.2 + - + +
134A GLU* 3.3 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 3.2 30.3 + - + +
105A GLU* 2.6 38.2 + - + +
106A LEU* 4.2 20.1 - - + +
109A LEU* 6.3 0.7 - - + -
122A PHE* 3.8 25.5 - + - -
124A SER* 4.7 0.2 + - - -
126A ASN 3.3 15.8 + - - -
127A VAL* 3.6 15.0 - - + -
128A THR* 2.9 36.2 + - - +
130A GLU* 1.3 81.3 - - - +
132A VAL* 1.3 64.7 + - - +
133A GLU 2.9 0.9 + - - -
134A GLU* 3.1 3.1 + - - +
135A LEU* 2.8 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 4.3 1.6 - - + +
128A THR 3.1 17.5 - - - +
129A GLU* 3.4 19.5 - - + +
131A HIS* 1.3 75.6 - - - +
133A GLU* 1.3 60.4 + - - +
135A LEU* 3.3 10.5 - - - +
136A LYS* 2.9 30.9 + - + +
149A GLU* 3.2 31.2 - - + +
151A THR* 4.6 1.1 - - + +
153A GLN* 3.2 35.7 - - + +
154A ILE* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 3.0 26.5 + - - +
130A GLU* 3.0 12.8 + - + +
131A HIS 2.9 0.2 + - - -
132A VAL* 1.3 82.4 - - - +
134A GLU* 1.3 69.0 + - - +
135A LEU 3.0 1.5 + - - -
136A LYS* 3.3 10.3 + - + +
137A LYS* 3.2 39.2 + - - +
153A GLN* 4.9 4.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
106A LEU* 3.7 39.5 - - + +
109A LEU* 5.9 8.2 - - + +
130A GLU* 3.3 7.4 + - + +
131A HIS 3.1 2.8 + - - +
133A GLU* 1.3 80.5 - - - +
135A LEU* 1.3 62.7 + - + +
137A LYS* 3.2 29.9 + - - +
138A SER* 3.2 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 6.5 1.3 - - + -
109A LEU* 4.4 22.2 - - + -
122A PHE* 4.4 21.3 - - + -
127A VAL* 4.3 22.9 - - + -
131A HIS* 2.8 19.4 + - + +
132A VAL* 3.3 8.1 - - + +
134A GLU* 1.3 73.4 - - + +
136A LYS* 1.3 56.8 - - - +
137A LYS 3.0 1.6 - - - -
138A SER* 2.7 34.5 + - - -
142A VAL* 4.0 30.9 - - + +
144A LEU* 4.5 0.9 - - + -
154A ILE* 3.4 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 2.9 21.7 + - + +
133A GLU* 3.3 9.8 + - - +
135A LEU* 1.3 74.1 - - - +
137A LYS* 1.3 61.6 + - + +
138A SER 3.5 3.1 + - - +
153A GLN* 2.8 54.5 - - - +
154A ILE* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 3.2 29.8 - - - +
134A GLU* 3.4 29.3 + - + +
135A LEU 3.0 0.8 - - - -
136A LYS* 1.3 75.6 - - + +
138A SER* 1.3 69.4 + - - +
139A PRO* 3.5 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.6 12.0 - - - +
113A LEU* 4.6 0.2 - - - +
134A GLU 3.2 8.2 + - - -
135A LEU* 2.7 20.9 + - - -
136A LYS 3.2 3.9 - - - +
137A LYS* 1.3 85.0 - - - +
139A PRO* 1.3 74.5 - - - +
140A VAL* 2.6 31.5 + - - +
142A VAL* 4.2 12.7 - - - +
----------------------------------------------------------
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