Contacts of the helix formed by residues 97 - 106 (chain A) in PDB entry 5DPT
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 97 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER 3.9 13.6 + - - +
61A ASP* 4.7 9.6 - - - +
62A LEU 3.6 8.1 - - - +
63A THR* 4.0 11.0 - - + +
64A VAL* 4.4 1.6 - - - -
95A SER 4.5 5.6 - - - +
96A ALA* 1.3 77.4 - - - +
98A MET* 1.3 59.1 + - - +
99A GLY* 3.6 1.4 + - - -
100A GLN* 3.1 43.2 + - - +
101A LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.2 8.5 - - + +
38A VAL* 3.7 30.5 - - + -
58A VAL* 3.8 21.1 - - + -
59A PRO 4.0 13.0 - - - +
60A SER* 4.1 0.6 + - - -
62A LEU 2.8 24.9 + - - +
63A THR 4.2 4.0 - - - +
64A VAL* 3.9 28.3 - - - -
67A PHE* 4.0 28.9 - - + -
97A THR* 1.3 73.4 - - - +
99A GLY* 1.3 57.5 - - - +
100A GLN 3.4 0.2 - - - -
101A LEU* 3.8 9.7 - - + +
102A TYR* 2.9 29.1 + - - +
112A LEU* 3.8 16.9 - - + +
114A VAL* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.6 5.2 - - - -
60A SER* 3.1 29.1 + - - -
97A THR* 3.1 1.7 - - - -
98A MET* 1.3 76.6 - - - +
100A GLN* 1.3 59.4 + - - +
102A TYR* 3.5 5.9 + - - +
103A GLU* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER 4.9 0.3 - - - +
96A ALA* 3.7 13.0 - - + +
97A THR* 3.1 44.9 + - - +
99A GLY* 1.3 75.7 - - - +
101A LEU* 1.3 61.9 + - - +
103A GLU* 3.6 10.6 + - - +
104A ASP* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.7 24.5 - - + -
85A PHE* 6.6 0.2 - - + -
87A VAL* 3.9 23.3 - - + -
92A PRO* 3.8 22.9 - - + -
93A PRO* 4.9 7.4 - - + -
96A ALA* 5.3 4.7 - - + +
97A THR 2.9 15.9 + - - +
98A MET* 3.9 13.7 - - + +
100A GLN* 1.3 75.9 - - - +
102A TYR* 1.3 59.2 + - - +
104A ASP* 3.4 3.1 + - + +
105A ASN* 2.9 52.7 + - - +
112A LEU* 4.0 18.3 - - + +
114A VAL* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.2 42.9 - - - -
36A VAL* 3.4 36.3 - - + -
37A PRO* 4.3 3.6 - - + -
98A MET 2.9 19.7 + - - +
99A GLY 3.8 4.5 - - - +
100A GLN 3.4 0.2 - - - -
101A LEU* 1.3 78.1 - - - +
103A GLU* 1.3 61.2 + - + +
106A HIS* 3.0 65.9 + + + +
110A TYR* 2.9 46.6 + + - +
112A LEU* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 5.0 1.0 + - - -
99A GLY 3.1 17.6 + - - +
100A GLN* 3.9 9.3 - - - +
101A LEU 3.4 0.2 - - - -
102A TYR* 1.3 80.6 - - + +
104A ASP* 1.3 71.0 + - - +
106A HIS* 3.9 15.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 2.9 20.4 + - - +
100A GLN* 3.1 20.2 + - - +
101A LEU* 4.0 5.2 - - + +
102A TYR 3.1 0.4 - - - -
103A GLU* 1.3 93.8 - - - +
105A ASN* 1.3 68.8 + - - +
31B LYS* 4.0 20.6 + - - -
32B TYR* 3.9 18.4 + - - +
35B ARG* 4.9 0.2 + - - -
57B LEU* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.3 7.2 - - - +
87A VAL* 3.4 36.2 + - + +
88A ASN* 3.2 22.9 + - - +
90A THR* 5.0 0.4 + - - -
92A PRO* 5.7 0.2 - - - +
101A LEU* 2.9 29.2 + - - +
104A ASP* 1.3 91.7 - - - +
106A HIS* 1.3 62.4 + - - +
107A GLU* 3.7 3.6 + - - +
111A PHE 4.6 0.7 - - - +
112A LEU* 3.6 11.5 - - + +
113A TYR* 4.8 2.8 + - - -
32B TYR* 3.7 17.5 + - - -
35B ARG* 3.2 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.0 22.2 + - - +
102A TYR* 3.0 64.1 + + + +
103A GLU* 3.9 17.9 + - - +
105A ASN* 1.3 78.3 - - - +
107A GLU* 1.3 83.2 + - - +
108A GLU* 4.8 9.3 - - - +
110A TYR* 4.2 23.5 - + - -
111A PHE 3.6 9.2 - - - +
112A LEU* 4.5 2.2 - - - +
----------------------------------------------------------
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