Contacts of the helix formed by residues 96 - 105 (chain K) in PDB entry 3SWD
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 96 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K PHE* 4.1 13.9 - - + -
33K LEU* 4.5 9.5 - - + +
56K LEU* 4.3 23.6 - - + -
60K LEU* 4.7 4.3 - - + -
82K ALA* 4.5 12.6 - - + -
93K SER 3.0 14.3 + - - +
94K ILE 2.8 1.2 + - - -
95K TRP* 1.3 75.7 - - - +
97K LEU* 1.3 70.1 + - - +
99K PRO* 3.2 11.5 - - - +
100K LEU* 3.4 19.9 + - + +
109K VAL* 4.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K ILE* 3.0 20.3 + - + +
96K ALA* 1.3 80.3 - - - +
98K GLY* 1.3 65.0 + - - +
100K LEU* 3.1 13.4 + - - +
101K VAL* 3.2 16.8 + - + +
107K GLY 3.3 32.3 - - - +
109K VAL* 3.3 23.2 - - + +
125K HIS* 6.0 3.1 - - + -
126K ILE* 5.7 4.0 - - + -
129K LEU* 3.5 26.2 - - + -
136K ILE* 5.4 2.2 - - + -
143K VAL* 4.2 29.6 - - + +
145K ALA* 3.6 17.3 - - + -
168K THR* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K ILE 4.5 0.8 + - - -
95K TRP 4.0 2.4 + - - -
97K LEU* 1.3 79.2 - - - +
99K PRO* 1.3 67.4 - - - +
101K VAL* 3.5 3.0 + - - +
102K ALA* 3.0 23.5 + - - +
129K LEU* 4.5 22.6 - - - +
168K THR* 4.5 14.6 - - - +
172K ALA* 4.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K PHE 3.5 20.9 - - - +
31K ALA* 4.9 2.2 - - - -
33K LEU* 3.9 24.2 - - + -
34K LEU* 3.7 27.1 - - + -
95K TRP 3.0 24.9 - - - +
96K ALA* 3.2 7.6 - - - +
98K GLY* 1.3 85.3 - - - +
100K LEU* 1.3 53.6 + - - +
102K ALA* 2.9 2.3 + - + +
103K ARG* 2.7 38.6 + - - +
168K THR* 6.5 0.2 - - - -
171K CYS* 4.9 13.0 - - + -
172K ALA* 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 5.0 9.9 - - + -
60K LEU* 3.9 21.3 - - + -
77K VAL* 4.5 8.3 - - + -
80K PHE* 3.2 46.0 - - + +
81K CYS* 5.1 0.9 - - - -
82K ALA* 5.8 0.9 - - + +
96K ALA* 3.4 17.0 + - + +
97K LEU* 3.1 11.0 + - - +
99K PRO* 1.3 78.9 - - - +
101K VAL* 1.3 54.6 + - - +
104K PHE* 2.7 63.8 + - + -
106K GLN 3.2 16.2 - - - +
107K GLY* 4.2 5.4 - - - -
108K GLN 5.1 1.6 - - - +
109K VAL* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K LEU* 3.2 21.8 + - + +
98K GLY* 4.1 4.7 - - - +
100K LEU* 1.3 73.7 - - - +
102K ALA* 1.3 61.7 + - - +
105K GLY* 3.2 21.7 + - - -
106K GLN 3.6 19.7 - - - +
107K GLY* 4.2 0.2 - - - -
129K LEU* 5.3 7.0 - - + -
134K ALA* 4.7 9.9 - - + -
145K ALA* 3.5 27.8 - - + -
146K SER* 4.2 15.3 - - - +
147K VAL* 3.6 26.9 - - + +
151K LEU* 4.7 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS* 5.4 2.4 + - - -
34K LEU* 3.5 19.3 - - + -
98K GLY 3.0 13.4 + - - +
99K PRO 2.9 9.4 + - - +
101K VAL* 1.3 80.8 - - - +
103K ARG* 1.3 60.2 + - - +
105K GLY 4.7 0.5 + - - -
150K ARG* 5.8 4.5 - - - +
151K LEU* 4.3 15.2 + - + +
172K ALA* 3.8 26.5 - - - +
175K LEU* 4.2 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS* 3.8 17.4 + - - -
33K LEU 3.4 24.2 + - - +
34K LEU* 4.2 8.5 + - + +
35K ALA 3.1 23.1 + - - -
36K GLU* 3.4 38.8 + - - +
74K ALA* 2.9 31.5 + - - +
75K ARG* 3.7 11.8 + - - +
77K VAL* 4.0 3.8 - - - +
99K PRO 2.7 18.0 + - - +
102K ALA* 1.3 75.7 - - - +
104K PHE* 1.3 98.2 + - + +
105K GLY 3.9 0.2 - - - -
175K LEU* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C HIS* 4.0 10.4 - - - +
287C LYS* 4.2 18.0 - - - +
33K LEU 4.9 2.2 - - - -
77K VAL* 3.8 25.1 - - + -
80K PHE* 3.4 39.3 - + + -
100K LEU* 2.7 43.9 + - + +
103K ARG* 1.3 124.0 - - + +
105K GLY* 1.3 61.4 + - - +
106K GLN* 3.4 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C HIS* 3.6 11.6 + - - -
287C LYS* 4.8 2.3 - - - +
101K VAL* 3.2 11.9 + - - -
102K ALA 4.7 0.6 + - - -
103K ARG 3.9 0.4 - - - -
104K PHE* 1.3 76.4 - - - +
106K GLN* 1.3 61.2 + - - +
146K SER* 3.1 7.1 - - - -
147K VAL* 2.9 53.8 + - - -
149K GLY 4.9 1.6 - - - -
----------------------------------------------------------
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