Contacts of the helix formed by residues 102 - 108 (chain A) in PDB entry 5ABT
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 1.3 74.3 - - - +
103A SER* 1.3 66.5 + - - +
104A THR 3.4 1.3 - - - -
105A ALA* 3.1 14.8 + - - +
106A MET* 3.2 13.0 + - - +
126A LEU* 5.0 1.0 - - - +
127A ALA* 3.4 26.4 - - + +
128A LEU* 6.2 0.2 - - - +
129A ASP* 5.2 2.7 - - + +
140A VAL* 5.9 0.4 - - + -
141A ALA 4.7 12.6 - - - +
142A VAL* 4.5 3.5 - - + +
145A TRP* 6.3 1.6 - - + +
156A LEU* 5.7 0.7 - - - +
1247A GUO 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.6 26.2 + - - -
102A ALA* 1.3 77.4 - - - +
104A THR* 1.3 59.1 + - - +
106A MET* 3.1 5.0 + - - +
107A LYS* 2.9 34.2 + - - +
142A VAL* 3.6 13.4 - - - +
143A SER* 2.8 31.4 + - - -
1247A GUO 2.6 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL 3.5 8.1 + - - -
83A ARG* 3.2 46.6 - - - +
101A ILE* 4.5 4.7 - - - +
102A ALA 3.4 0.2 - - - -
103A SER* 1.3 77.5 - - - +
105A ALA* 1.3 58.3 + - - +
107A LYS* 4.2 6.3 - - + +
108A SER* 2.8 41.4 + - - +
111A VAL* 4.8 3.8 - - + -
112A VAL* 3.5 19.1 - - + +
115A TRP* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 4.1 14.1 - - + +
102A ALA 3.1 10.6 + - - +
104A THR* 1.3 80.1 - - - +
106A MET* 1.3 58.7 + - - +
109A PRO* 4.1 4.9 - - - +
112A VAL* 3.7 12.9 - - + +
126A LEU* 3.5 30.3 - - + -
156A LEU* 3.7 6.5 - - + +
160A TYR* 2.5 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.2 5.6 + - - +
103A SER 3.1 8.3 + - - +
105A ALA* 1.3 79.3 - - - +
107A LYS* 1.3 94.3 + - + +
108A SER 3.6 0.2 + - - -
109A PRO* 3.8 10.9 - - - +
140A VAL* 5.1 0.2 - - + -
142A VAL* 3.9 15.3 - - + -
149A SER* 3.7 45.1 - - - +
151A VAL* 3.7 18.8 - - + -
156A LEU* 3.9 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 2.9 23.8 + - - +
104A THR* 4.3 5.2 - - - +
106A MET* 1.3 101.6 - - + +
108A SER* 1.3 67.8 + - - +
109A PRO* 3.6 5.1 - - - +
142A VAL* 4.3 11.2 - - + +
143A SER* 4.6 3.4 + - - -
147A GLU* 3.2 28.6 + - - -
149A SER* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 2.8 27.0 + - - +
107A LYS* 1.3 88.5 + - - +
109A PRO* 1.3 66.2 - - - +
110A ASP 3.3 2.7 - - - -
111A VAL* 3.1 25.8 + - - +
112A VAL* 3.1 17.3 + - - +
----------------------------------------------------------
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