Contacts of the helix formed by residues 124 - 136 (chain A) in PDB entry 1LTM
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 PRO 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 1.3 84.9 - - - +
125A ASP* 1.3 58.1 + - - +
127A VAL* 3.4 5.6 + - + +
128A GLN* 2.9 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 3.2 6.9 + - - +
124A PRO* 1.3 80.7 - - - +
126A ASN* 1.3 59.5 + - - +
128A GLN* 3.8 11.3 + - - +
129A ASN* 3.0 54.9 + - - +
164A ARG* 4.3 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS 4.1 6.5 + - - -
121A PHE* 2.9 43.5 + - - +
123A THR* 3.1 17.7 + - - +
125A ASP* 1.3 78.3 - - - +
127A VAL* 1.3 60.1 + - - +
129A ASN* 3.2 3.0 + - - -
130A GLY 2.8 25.5 + - - -
160A GLY 5.5 1.6 + - - -
164A ARG* 3.6 37.1 + - - +
165A TRP* 3.1 28.3 - - + -
351A LEU* 4.7 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.3 10.8 - - + -
123A THR 2.9 22.8 + - - +
124A PRO* 3.9 5.2 - - + +
126A ASN* 1.3 74.5 - - - +
128A GLN* 1.3 60.2 + - + +
130A GLY* 3.1 2.3 + - - -
131A VAL* 2.9 32.1 + - - +
351A LEU* 4.3 11.2 - - + -
354A ALA* 3.8 34.5 - - + +
355A VAL* 3.7 9.2 - - - +
358A ALA* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 2.9 41.2 + - - +
125A ASP* 3.8 11.6 + - - +
127A VAL* 1.3 78.6 - - + +
129A ASN* 1.3 63.7 + - - +
131A VAL* 3.2 10.9 + - + +
132A VAL* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP* 3.0 42.7 + - - +
126A ASN* 3.8 6.8 + - - +
128A GLN* 1.3 74.9 - - - +
130A GLY* 1.3 60.0 + - - +
132A VAL* 3.3 11.0 + - - +
133A PHE* 3.0 28.4 + - - +
164A ARG* 4.5 4.4 - - - +
165A TRP* 4.0 10.1 - - + -
167A ARG* 3.4 49.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN 2.8 10.1 + - - -
127A VAL 3.1 4.7 + - - -
129A ASN* 1.3 76.2 - - - +
131A VAL* 1.3 63.6 + - - +
133A PHE* 3.3 2.3 + - - +
134A TRP* 3.0 24.9 + - - +
156A VAL* 4.1 3.0 - - - +
165A TRP* 3.5 31.8 - - - -
355A VAL* 3.5 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL 2.9 19.9 + - - +
128A GLN* 3.2 11.2 + - + +
130A GLY* 1.3 76.9 - - - +
132A VAL* 1.3 65.0 + - + +
134A TRP* 3.3 2.1 + - - +
135A ASN* 3.0 42.8 + - - +
355A VAL* 3.8 17.7 - - + +
358A ALA* 3.6 32.8 - - + +
359A ARG* 3.9 17.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
128A GLN* 3.1 15.9 + - + +
129A ASN* 3.3 14.6 + - - +
131A VAL* 1.3 78.4 - - + +
133A PHE* 1.3 62.4 + - - +
135A ASN* 3.9 5.4 - - - +
136A GLN* 3.0 34.9 + - + +
167A ARG* 5.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASN 3.0 15.9 + - - +
130A GLY 3.7 3.1 - - - +
131A VAL 3.3 0.2 - - - -
132A VAL* 1.3 78.1 - - - +
134A TRP* 1.3 67.5 + - - +
136A GLN* 3.3 7.7 + - - -
137A TYR* 2.9 54.8 + + + +
141A LEU* 4.8 2.9 - - + -
156A VAL* 4.3 15.5 - - + -
159A ILE* 4.1 22.4 - - + -
165A TRP* 3.3 47.1 - + + -
223A TYR* 4.3 22.0 - + - -
249A PRO* 4.4 4.3 - - + -
253A ILE* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 3.0 15.5 + - - +
131A VAL* 3.6 4.7 - - - +
133A PHE* 1.3 79.6 - - - +
135A ASN* 1.3 55.6 + - - +
137A TYR 3.3 1.4 + - - -
138A GLU* 2.9 37.1 + - + +
141A LEU* 3.7 19.6 - - + +
142A ASN* 5.6 1.2 + - - -
152A PRO* 3.4 24.7 - - + +
153A GLU* 3.8 33.4 - - - -
156A VAL* 3.8 15.9 - - + -
352A GLY 4.1 2.0 - - - -
355A VAL* 3.5 18.6 - - + -
356A ALA* 3.6 39.9 - - + -
359A ARG* 3.3 46.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.0 36.6 + - - +
132A VAL* 3.9 5.7 - - - +
134A TRP* 1.3 74.4 - - - +
136A GLN* 1.3 64.9 + - - +
137A TYR 3.4 0.3 + - - -
138A GLU* 3.4 20.7 + - - +
359A ARG* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 3.0 29.9 + - + +
133A PHE* 3.6 7.0 - - - +
135A ASN* 1.3 78.1 - - - +
137A TYR* 1.3 99.7 + - + +
138A GLU 3.7 0.3 + - - -
139A ASP 5.4 0.2 + - - -
----------------------------------------------------------
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