Contacts of the strand formed by residues 112 - 120 (chain E) in PDB entry 4P5K
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 112 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E PRO* 3.3 3.3 - - - +
102E SER* 2.8 54.6 + - - +
110E HIS* 4.1 30.3 - - + +
111E ASN* 1.3 77.2 + - - +
113E LEU* 1.3 61.4 + - - +
114E VAL* 4.4 3.4 - - + +
141E VAL* 6.3 2.9 - - + -
158E MET* 4.4 35.4 - - + -
159E LEU 3.6 4.5 - - - +
160E GLU* 3.8 29.6 - - + +
161E MET* 3.9 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E VAL* 4.0 12.3 - - + -
100E SER 3.8 6.1 - - - +
101E PRO* 4.4 8.5 - - + -
112E LEU* 1.3 72.7 - - - +
114E VAL* 1.3 60.4 + - - +
129E TRP* 3.7 26.0 - - + -
158E MET* 3.1 4.7 - - - +
159E LEU* 2.7 42.9 + - + +
161E MET* 4.0 23.5 - - + +
169E TYR* 3.7 43.3 - - + -
186E TRP* 3.8 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ASN 3.3 2.3 - - - +
99E VAL* 3.1 26.4 - - - +
100E SER* 2.7 25.6 + - - +
101E PRO 4.7 6.5 - - - +
102E SER* 4.9 8.1 - - - +
112E LEU* 4.4 9.9 - - + +
113E LEU* 1.3 77.8 - - - +
115E CYS* 1.3 62.5 + - - +
116E HIS* 4.3 8.3 - - + +
129E TRP* 4.3 2.7 - - - -
156E LEU* 4.1 25.8 - - + -
157E VAL 3.8 4.9 - - - +
158E MET* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E VAL* 3.5 22.9 - - - -
98E ASN 3.5 2.7 - - - -
99E VAL* 4.3 2.2 - - + -
114E VAL* 1.3 71.8 - - - +
116E HIS* 1.3 62.4 + - - +
117E VAL* 3.4 18.2 + - - +
127E VAL* 4.6 1.1 - - - -
129E TRP* 3.6 14.1 - - + +
156E LEU* 3.7 1.0 - - - -
157E VAL* 2.8 39.0 + - + +
171E CYS* 2.0 49.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PRO* 4.7 6.3 + - - +
94D LYS 4.8 0.2 - - - -
95D GLU 4.2 3.6 + - - -
96D PRO* 3.6 34.8 - - + +
96E ARG 3.6 1.6 - - - +
97E VAL* 3.4 2.8 - - - -
98E ASN* 2.8 51.4 + - + +
114E VAL* 3.8 5.6 - - + +
115E CYS* 1.3 71.0 - - - +
117E VAL* 1.3 64.0 + - - +
118E THR* 3.4 18.4 + - + +
154E GLN* 2.5 32.5 + - + -
155E ILE 3.8 2.4 + - - -
156E LEU* 3.2 37.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E PRO* 4.0 14.8 - - + -
96E ARG 3.3 6.1 - - - +
97E VAL* 4.1 2.7 - - + -
115E CYS* 3.6 29.2 - - - +
116E HIS* 1.3 77.4 + - - +
118E THR* 1.3 61.9 + - - +
120E PHE* 3.5 20.4 - - + -
125E ILE* 4.1 12.3 - - + -
127E VAL* 4.6 11.4 - - + -
154E GLN* 3.1 4.7 - - - +
155E ILE* 3.0 44.3 + - + +
173E VAL* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS 3.5 20.6 - - - +
95D GLU* 4.4 2.8 + - - -
96D PRO* 4.1 16.3 - - + +
95E PRO* 3.3 2.9 - - - +
96E ARG* 2.9 47.1 + - - +
116E HIS* 3.4 36.1 + - + +
117E VAL* 1.3 75.7 - - - +
119E ASP* 1.3 74.9 + - - +
120E PHE* 3.2 5.0 + - - -
153E PHE 3.4 7.0 - - - -
154E GLN* 3.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS* 3.4 30.1 + - - +
95D GLU* 3.1 33.4 - - - +
93E VAL* 3.3 24.2 - - + +
94E GLN 3.5 5.4 - - - +
96E ARG* 4.0 21.8 - - + -
118E THR* 1.3 80.6 + - - +
120E PHE* 1.3 59.2 + - - +
148E ASN* 4.5 1.9 + - - +
152E THR* 3.9 17.1 + - + +
153E PHE 2.8 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL* 3.2 12.3 - - - +
95E PRO* 3.6 20.0 - - + -
117E VAL* 3.5 40.4 - - + -
118E THR 3.7 10.3 - - - -
119E ASP* 1.3 80.8 - - - +
121E TYR* 1.3 61.3 + - - +
122E PRO 3.3 24.5 - - - -
123E GLY 3.9 14.1 - - - -
125E ILE* 3.8 26.0 - - + -
145E LEU* 4.2 4.5 - - + -
152E THR* 3.6 2.1 - - - -
153E PHE* 2.9 56.3 + - + -
154E GLN* 3.7 11.0 - - - -
155E ILE* 4.2 2.9 - - + -
175E HIS* 3.8 9.6 - - - +
----------------------------------------------------------
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