Contacts of the helix formed by residues 121 - 125 (chain B) in PDB entry 4MCA
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 ASP 121 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 1.3 71.2 - - - +
122B ALA* 1.3 59.7 + - - +
123B PRO* 3.2 9.2 - - - +
124B THR* 4.0 4.7 + - - -
171B ASP* 3.1 8.1 + - + +
237B ASN 3.5 8.1 - - - +
238B THR 4.4 2.9 - - - +
241B SER* 2.6 33.0 + - - +
242B GLY* 3.6 20.9 - - - +
245B PHE* 3.6 18.3 - - - -
1001B GOL 2.3 32.7 + - - -
1004B NA 2.5 28.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY* 6.5 1.8 - - - -
97B LEU* 6.5 0.2 - - + -
98B ASP* 5.2 8.1 - - - +
101B LYS* 2.9 14.4 + - - +
120B THR* 3.2 15.6 + - - +
121B ASP* 1.3 80.3 + - - +
123B PRO* 1.4 64.4 - - + +
125B SER* 2.6 28.0 + - - +
127B LEU* 5.3 3.1 - - + +
128B SER* 6.5 0.4 - - - -
129B VAL* 6.3 1.8 - - + -
245B PHE* 4.8 0.2 - - - -
1001B GOL 3.8 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.2 17.5 - - + -
101B LYS* 3.7 5.6 - - - +
113B LEU* 3.4 14.3 - - + +
115B PRO* 4.0 29.6 - - + -
117B ILE 6.0 0.2 - - - +
120B THR* 3.5 15.0 - - - +
121B ASP* 3.2 7.4 - - - +
122B ALA* 1.4 93.4 - - + +
124B THR* 1.3 61.0 + - - +
125B SER 3.3 0.2 + - - -
147B PRO* 3.2 20.1 - - - +
150B VAL* 3.9 14.7 - - + +
152B MET* 5.7 0.9 - - + -
238B THR* 4.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.6 28.0 - - + +
11B TYR* 4.4 7.0 - - + -
121B ASP 4.0 0.5 + - - -
122B ALA 3.2 0.2 + - - -
123B PRO* 1.3 77.8 - - - +
125B SER* 1.3 53.1 + - - +
146B ASN* 2.7 28.1 + - - -
147B PRO* 3.5 7.9 - - - +
150B VAL* 4.3 11.0 - - + -
238B THR* 3.8 26.1 + - + +
239B TYR* 4.2 18.4 - - + -
242B GLY* 3.4 31.7 - - - -
243B ILE* 4.1 4.0 + - - +
246B GLU* 4.4 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 2.8 27.0 + - - -
122B ALA* 2.6 24.2 + - - -
124B THR* 1.3 82.6 + - - +
126B ALA* 1.3 58.5 + - - +
127B LEU* 3.2 21.7 + - - +
146B ASN* 3.7 2.5 - - - +
147B PRO* 3.3 6.8 - - - +
242B GLY 5.3 0.2 - - - -
245B PHE* 3.7 29.9 - - - -
246B GLU* 3.6 14.8 - - - -
----------------------------------------------------------
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