Contacts of the strand formed by residues 108 - 116 (chain G) in PDB entry 4PKI
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 LEU 108 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLY 3.1 27.1 - - - +
64G LYS 4.0 16.4 - - - +
65G GLU* 4.3 0.4 - - - -
66G PRO* 4.2 9.2 - - + -
100G THR* 3.6 24.5 - - + -
101G VAL 3.4 1.8 - - - -
102G GLN* 3.5 41.1 - - + +
106G GLY 4.1 5.4 - - - +
107G ASN* 1.3 80.2 + - - +
109G GLN* 1.3 60.8 + - - +
110G TYR* 3.7 15.7 - - + +
142G ARG* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G LYS 3.4 1.2 - - - +
100G THR* 3.3 6.6 - - - -
101G VAL* 2.6 62.5 + - + +
103G LEU* 5.0 16.9 - - + +
107G ASN 4.0 0.8 + - - -
108G LEU* 1.3 73.2 - - - +
110G TYR* 1.3 66.0 + - - +
111G ASP* 3.3 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLY* 2.8 40.6 + - - -
64G LYS* 5.4 1.6 + - - -
98G LEU* 4.0 13.2 - - + -
99G LYS 3.5 1.3 - - - -
100G THR* 3.7 20.4 - - + -
108G LEU* 3.7 16.5 - - + +
109G GLN* 1.3 81.1 - - - +
111G ASP* 1.3 66.4 + - - +
139G LEU* 3.9 32.7 - - + +
142G ARG* 3.4 50.7 + - + +
143G ALA* 3.4 20.7 - - + +
144G VAL* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LEU* 3.5 5.7 - - - +
99G LYS* 2.9 39.6 + - + +
101G VAL* 5.7 1.2 - - - +
109G GLN* 3.3 24.8 - - - +
110G TYR* 1.3 79.1 - - - +
112G LEU* 1.3 60.0 + - - +
113G HIS* 3.6 12.2 - - - +
144G VAL* 3.5 13.6 - - - +
146G HIS* 3.0 23.2 + - - +
156G THR* 5.9 3.0 - - - +
160G TYR* 3.8 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G VAL* 4.0 12.8 - - + -
97G ILE 3.5 13.0 - - - +
98G LEU* 3.9 24.7 - - + -
110G TYR 4.2 0.6 - - - -
111G ASP* 1.3 70.2 - - - +
113G HIS* 1.3 56.8 + - - +
132G THR* 3.6 40.1 - - + +
135G LEU* 3.9 28.3 - - + -
136G ASP* 3.8 16.6 - - + +
139G LEU* 5.2 0.2 - - + -
143G ALA* 3.8 17.0 - - + -
144G VAL 2.7 13.9 + - - +
145G GLN* 3.3 3.6 - - + +
146G HIS* 2.6 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G VAL* 3.6 1.9 - - - +
97G ILE* 2.7 46.4 + - + +
111G ASP* 3.6 16.5 - - - +
112G LEU* 1.3 80.0 - - - +
114G TYR* 1.3 60.0 + - - +
132G THR* 4.9 2.0 - - - -
146G HIS* 3.2 33.9 - + - +
148G GLU* 2.7 33.4 + - + -
154G SER* 4.4 3.4 - - - -
156G THR* 4.6 6.5 - - + +
157G PHE* 3.6 35.5 - + + -
160G TYR* 2.8 34.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY 3.2 24.7 - - - -
147A ARG* 3.4 5.0 - - - +
148A THR* 2.9 47.4 + - + -
149A THR 4.5 1.2 + - - -
95G TYR 3.2 10.8 - - - +
96G VAL* 4.5 1.3 - - + +
113G HIS* 1.3 72.0 - - - +
115G TRP* 1.3 61.5 + - - +
116G LEU* 3.9 12.4 + - + +
128G ALA* 4.1 12.1 - - + +
129G ALA* 4.3 11.7 - - + -
132G THR* 3.5 33.2 - - + +
145G GLN* 4.9 0.9 - - + -
146G HIS 2.9 27.8 + - - -
147G ARG* 3.5 27.6 - - + +
148G GLU* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G PHE* 3.7 26.2 - + + -
90G PHE 3.4 23.8 - - - -
91G THR* 4.1 3.8 - - - -
93G ASP 3.7 1.8 - - - -
94G ALA* 3.3 3.5 - - - -
95G TYR* 2.9 49.8 + + + +
97G ILE* 4.0 19.5 - - + -
113G HIS 4.0 0.8 - - - -
114G TYR* 1.3 71.9 - - - +
116G LEU* 1.3 61.8 + - - +
117G GLY* 3.4 23.6 - - - -
148G GLU* 3.2 14.6 - - + -
150G GLN* 3.8 23.9 - - + +
153G GLU* 2.9 37.8 + - + +
157G PHE* 3.8 20.7 - + + -
165G LEU* 4.9 1.8 - - - +
167G TYR* 3.7 26.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 3.7 11.9 - - - +
93G ASP 4.5 0.9 - - - -
94G ALA* 3.9 9.0 - - + -
114G TYR* 4.4 9.2 - - + +
115G TRP* 1.3 81.5 - - - +
117G GLY* 1.3 64.9 + - - +
118G ASN* 4.8 0.2 - - - -
120G CYS* 4.4 6.5 - - - -
125G SER* 3.5 38.6 - - - +
128G ALA* 4.3 9.4 - - + -
147G ARG* 3.6 40.6 - - + +
148G GLU 2.9 14.5 + - - +
149G VAL* 3.8 8.5 - - + +
150G GLN* 3.1 23.6 + - - +
----------------------------------------------------------
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