Contacts of the helix formed by residues 121 - 133 (chain A) in PDB entry 4MEI
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 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 1.3 73.6 - - - +
122A PRO* 1.3 69.3 - - - +
123A LYS* 4.1 4.2 + - - +
124A GLU* 3.0 12.6 + - - +
125A GLN* 2.7 30.4 + - - +
210A GLN* 3.3 14.9 + - - -
211A VAL 3.1 19.3 + - - -
212A SER* 3.4 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER 4.4 0.9 - - - +
121A SER* 1.3 86.4 - - - +
123A LYS* 1.3 61.3 + - + +
125A GLN* 3.4 8.1 + - + +
126A ASN* 3.3 20.3 + - - +
210A GLN* 4.0 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 3.3 5.2 + - - +
122A PRO* 1.3 79.6 - - + +
124A GLU* 1.3 60.2 + - - +
126A ASN* 3.7 6.6 + - - +
127A ARG* 3.5 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 4.0 15.5 - - - +
101A ARG* 2.9 33.0 + - - +
120A SER* 4.1 1.3 - - - -
121A SER* 3.0 13.7 + - - +
123A LYS* 1.3 73.4 - - - +
125A GLN* 1.3 66.3 + - - +
126A ASN 3.1 1.6 - - - -
127A ARG* 2.5 46.4 + - - +
128A PHE* 3.0 22.5 + - - +
211A VAL* 3.3 29.6 - - + +
212A SER 3.7 7.3 - - - +
213A GLU* 3.9 4.5 - - - -
214A TYR* 3.8 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.2 16.4 - - - -
117A SER* 3.0 48.2 + - - +
120A SER* 3.8 9.8 - - - -
121A SER 2.7 23.3 + - - +
122A PRO* 3.6 8.8 - - + +
124A GLU* 1.3 72.8 - - - +
126A ASN* 1.3 62.8 + - - +
128A PHE* 3.5 6.3 + - - +
129A ALA* 2.9 30.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
122A PRO 3.3 13.0 + - - +
123A LYS* 3.9 7.1 - - - +
124A GLU 3.1 0.8 - - - -
125A GLN* 1.3 83.7 + - - +
127A ARG* 1.3 67.3 + - - +
129A ALA* 3.4 7.5 + - - +
130A LYS* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 5.3 1.6 - - - +
123A LYS* 3.5 24.9 + - - +
124A GLU* 2.5 47.6 + - - +
126A ASN* 1.3 76.0 - - - +
128A PHE* 1.3 65.4 + - - +
130A LYS* 3.2 7.2 + - - +
131A TRP* 3.0 23.3 + - - +
212A SER 3.0 20.8 + - - -
213A GLU* 4.4 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.8 46.7 - - + +
112A SER 4.8 0.7 - - - -
113A PHE* 3.7 37.2 - + - -
116A VAL* 3.7 43.3 - - + -
117A SER* 4.0 11.2 - - - -
120A SER* 5.1 0.7 - - - +
124A GLU* 3.0 18.6 + - - +
125A GLN* 3.5 7.9 - - - +
127A ARG* 1.3 74.4 - - - +
129A ALA* 1.3 59.6 + - - +
131A TRP* 3.1 16.4 + + - +
132A TYR* 2.8 57.2 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.4 13.3 - - + -
125A GLN* 2.9 30.8 + - - +
126A ASN* 3.8 11.7 - - - +
127A ARG 3.3 0.2 - - - -
128A PHE* 1.3 78.4 - - - +
130A LYS* 1.3 65.8 + - - +
132A TYR* 3.1 4.7 + - - +
133A ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.1 19.8 + - - +
127A ARG* 3.2 5.8 + - - +
129A ALA* 1.3 76.4 - - - +
131A TRP* 1.3 61.7 + - - +
133A ALA* 3.6 14.6 + - - +
136A ASN* 3.2 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.8 32.8 - - + +
102A GLU* 4.5 15.9 - - - -
127A ARG 3.0 13.1 + - - +
128A PHE* 3.5 37.5 - + - +
130A LYS* 1.3 80.1 - - - +
132A TYR* 1.3 61.8 + + - +
136A ASN* 3.2 20.5 + - - +
138A GLU* 3.4 31.4 + - + +
139A SER* 3.3 15.8 - - - -
140A PRO* 3.4 36.6 - - + -
143A ILE* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 5.9 2.7 - - - -
101A ARG* 5.7 2.0 - - - -
104A PHE* 3.9 11.3 - + - -
109A ALA* 3.4 36.3 + - + +
112A SER* 5.3 3.4 - - - -
113A PHE* 3.5 39.9 + + + -
128A PHE* 2.8 43.4 + + + +
129A ALA 3.1 3.1 + - - +
131A TRP* 1.3 74.0 - + + +
133A ALA* 1.3 67.7 + - - +
139A SER* 2.8 16.4 + - - -
140A PRO* 4.1 30.3 - - + -
141A GLN* 3.0 39.9 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
129A ALA 3.0 15.5 + - - +
130A LYS* 3.7 12.1 - - - +
131A TRP 3.4 2.0 - - - -
132A TYR* 1.3 77.6 - - - +
134A GLY* 1.3 54.0 + - - +
135A ASN* 3.1 9.0 - - + +
136A ASN* 2.8 34.4 + - + +
139A SER* 3.8 3.1 - - - -
141A GLN* 4.5 0.4 - - - +
----------------------------------------------------------
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