Contacts of the strand formed by residues 104 - 116 (chain A) in PDB entry 3PIK
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 104 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 3.5 1.8 - - - +
93A TRP* 3.4 1.6 - - - -
94A SER* 2.7 48.5 + - - +
95A GLY* 4.7 0.7 - - - -
102A ALA 3.6 4.7 + - - -
103A THR* 1.3 78.6 - - - +
105A ARG* 1.3 69.8 + - - +
106A GLU* 5.1 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 3.3 4.9 - - - +
93A TRP* 3.3 38.9 - - + +
103A THR* 4.1 4.2 + - + +
104A THR* 1.3 83.6 - - - +
106A GLU* 1.3 64.9 + - - +
107A PHE* 3.9 23.7 - - + -
302A SER* 2.9 48.7 + - - +
303A ASP* 3.7 16.7 - - - +
304A LEU 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 4.7 0.2 - - - -
91A GLY* 3.6 1.6 - - - -
92A SER* 2.8 44.8 + - - +
104A THR* 5.5 5.0 - - + +
105A ARG* 1.3 81.5 - - - +
107A PHE* 1.3 69.8 + - - +
108A SER* 4.4 4.5 + - - +
300A ALA* 3.3 14.7 - - + +
301A SER* 3.1 34.8 + - - -
302A SER* 3.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 3.5 5.6 - - - +
91A GLY* 3.8 15.3 - - - -
93A TRP* 3.7 38.1 - + - -
105A ARG* 3.9 27.8 - - + -
106A GLU* 1.3 76.7 - - - +
108A SER* 1.3 63.2 + - - +
300A ALA* 3.0 6.2 - - - +
301A SER 2.7 38.5 + - - +
302A SER 4.2 0.9 - - - -
303A ASP* 3.8 14.4 - - - -
304A LEU* 3.3 51.6 - - + -
307A LEU* 4.1 15.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
89A GLY* 3.6 1.4 - - - -
90A SER* 3.0 47.6 + - - +
106A GLU* 5.1 4.6 + - - +
107A PHE* 1.3 75.8 - - - +
109A THR* 1.3 68.4 + - - +
110A GLY 4.3 0.2 - - - -
298A SER* 5.6 1.8 - - - -
299A THR 3.3 14.4 - - - -
300A ALA* 4.2 6.5 - - - +
307A LEU* 4.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU 3.3 15.5 - - - +
89A GLY* 4.6 3.6 - - - -
108A SER* 1.3 80.2 + - - +
110A GLY* 1.3 61.3 + - - +
297A ILE 4.0 0.5 - - - +
298A SER* 3.3 5.2 - - - -
299A THR* 3.0 44.4 + - - +
307A LEU* 3.6 19.2 - - - +
308A PHE* 4.2 23.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN 3.9 0.3 - - - +
87A GLY* 3.4 4.0 - - - -
88A GLU* 2.8 43.7 + - - +
108A SER 4.3 0.2 - - - -
109A THR* 1.3 76.2 - - - +
111A LEU* 1.3 61.7 + - - +
112A ASN* 4.0 11.0 - - - -
297A ILE 3.6 4.7 - - - -
298A SER* 4.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.2 25.2 - - + +
86A ASN 3.5 18.2 - - - +
87A GLY* 4.3 6.3 - - - +
110A GLY* 1.3 73.7 - - - +
112A ASN* 1.3 60.3 + - - +
295A SER 4.1 0.2 - - - +
296A GLY* 3.2 3.1 - - - -
297A ILE* 2.8 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN 3.7 1.0 - - - +
85A LEU* 3.3 6.9 - - - +
86A ASN* 2.9 49.6 + - - +
88A GLU* 4.5 19.1 + - - +
110A GLY* 4.0 14.6 - - - +
111A LEU* 1.3 77.9 - - - +
113A ALA* 1.3 63.7 + - - +
114A SER* 5.4 0.7 - - - -
294A THR* 6.0 2.5 - - - -
295A SER 3.5 8.1 - - - +
296A GLY* 4.4 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 5.9 3.4 - - + -
84A GLN 3.0 10.5 - - - +
85A LEU* 3.9 12.5 - - + +
112A ASN* 1.3 75.7 - - - +
114A SER* 1.3 63.7 + - - +
293A LEU 4.5 0.2 - - - -
294A THR* 3.3 8.5 - - - -
295A SER* 2.8 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR 4.7 0.2 - - - +
83A PRO* 3.0 8.4 - - - +
84A GLN* 2.8 51.0 + - - +
112A ASN* 5.4 0.7 - - - -
113A ALA* 1.3 77.0 - - - +
115A PHE* 1.3 62.3 + - - +
116A ASP* 5.6 1.2 + - - -
293A LEU 3.4 5.2 - - - -
294A THR* 3.7 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG 3.6 18.8 - - - -
82A TYR 4.3 1.1 - - - -
83A PRO* 3.5 37.9 - - + -
114A SER* 1.3 76.5 + - - +
116A ASP* 1.3 82.0 + - - +
117A LEU* 3.6 35.9 + - + -
292A SER* 3.5 1.7 - - - -
293A LEU* 2.8 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP 5.0 2.9 - - - +
81A ARG 4.4 5.4 + - - +
82A TYR 5.7 0.6 + - - -
114A SER* 5.6 0.9 + - - -
115A PHE* 1.3 93.3 + - - +
117A LEU* 1.3 63.8 + - - +
118A ASP* 3.5 7.9 + - - +
122A ARG* 5.3 4.3 + - - -
123A LEU* 3.8 29.8 - - + +
291A ILE 4.0 4.3 - - - +
292A SER* 3.6 20.0 - - - -
----------------------------------------------------------
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