Contacts of the strand formed by residues 119 - 134 (chain E) in PDB entry 2IVB
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 GLY 119 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E VAL* 4.6 0.8 - - - +
113E HIS* 3.5 6.6 + - - -
117E GLY 3.5 1.5 + - - -
118E ASP* 1.3 84.1 + - - +
120E ILE* 1.3 64.1 + - - -
150E TYR* 4.0 5.8 - - - -
151E LEU 3.3 11.2 - - - -
153E THR* 3.6 16.4 - - - -
81F ARG* 5.5 1.2 + - - -
124F ILE* 4.5 0.7 - - - -
93G THR* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E VAL* 4.9 1.1 - - - -
119E GLY* 1.3 79.9 - - - +
121E ILE* 1.3 63.9 + - - +
122E ALA* 3.8 18.6 - - + +
150E TYR* 3.4 6.9 - - - -
151E LEU* 2.8 45.6 + - + +
124F ILE* 3.7 27.6 - - + -
92G PRO* 3.9 11.9 - - + +
93G THR* 3.8 27.4 - - - +
96G ARG* 3.6 13.2 - - + +
1161G AZI 3.3 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E VAL* 3.6 36.9 - - + +
116E PHE* 4.2 6.7 - - + -
120E ILE* 1.3 77.2 - - - +
122E ALA* 1.3 64.6 + - - +
123E ALA 3.4 1.0 + - - -
126E PHE* 6.0 2.5 - - + -
148E GLY* 4.2 18.4 - - - -
149E LYS 3.6 2.0 - - - +
150E TYR* 3.9 20.2 - - + -
93G THR* 5.2 3.4 + - - +
96G ARG* 3.3 26.2 - - - +
97G PHE* 4.5 15.8 - - + -
142G ALA* 3.4 36.6 - - + -
144G ILE* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ILE* 3.8 3.2 - - - -
121E ILE* 1.3 71.0 - - - +
123E ALA* 1.4 59.5 + - - +
124E ILE* 3.2 3.3 + - + -
125E ASN* 3.0 40.2 + - + +
126E PHE* 4.3 4.5 - - - -
148E GLY* 4.4 0.5 - - - -
149E LYS 2.8 19.6 + - - +
151E LEU* 3.4 33.7 - - + -
151F LEU* 5.4 1.6 - - + -
1161G AZI 3.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE 3.4 5.3 + - - -
122E ALA* 1.4 69.6 - - - +
124E ILE* 1.3 61.6 + - + +
126E PHE* 3.8 26.5 - - - +
96G ARG* 3.9 31.6 - - + +
99G GLU* 3.4 29.2 - - + +
100G MET* 5.0 6.3 - - + +
103G VAL* 6.1 0.7 - - - +
104G TYR* 5.5 2.9 - - - -
1161G AZI 3.3 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 3.9 28.5 - - + -
96B ARG* 4.1 4.9 - - - +
81E ARG* 6.1 2.7 - - - +
122E ALA* 3.2 1.5 + - + -
123E ALA* 1.3 81.6 - - + +
125E ASN* 1.3 61.0 + - + +
126E PHE* 3.4 8.6 + - - +
119F GLY* 4.2 1.8 - - - -
120F ILE* 3.5 34.5 - - + -
151F LEU* 3.6 22.4 - - + +
152F PRO 3.3 20.2 - - - +
153F THR* 3.0 41.3 + - + +
154F LYS 4.9 1.6 + - - +
99G GLU* 4.1 5.4 - - - +
1161G AZI 4.0 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ALA* 3.0 26.1 + - + +
124E ILE* 1.3 77.1 - - + +
126E PHE* 1.4 59.9 + - - +
148E GLY* 3.5 14.6 - - - -
149E LYS* 3.8 31.7 + - + +
151E LEU* 5.9 2.7 - - + +
151F LEU* 6.0 8.6 - - + +
152F PRO 4.8 6.5 - - - +
135G ASP* 5.2 1.4 + - - -
141G ARG* 3.3 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 6.0 2.7 - - + -
122E ALA 4.3 6.7 - - - -
123E ALA* 3.8 22.0 - - - +
124E ILE 3.4 8.1 + - - +
125E ASN* 1.4 79.5 + - - +
127E LYS* 1.3 73.6 + - - +
128E LEU* 3.9 24.2 - - + -
146E LEU* 3.7 41.1 - - + -
147E ASP 3.5 23.3 - - - -
148E GLY* 4.2 5.2 - - - -
154F LYS 5.1 2.8 - - - +
156F PHE* 3.6 19.2 - - + +
100G MET* 4.4 10.5 - - + -
104G TYR* 3.8 32.1 - + - +
141G ARG* 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA* 5.8 1.6 - - - -
126E PHE* 1.3 81.3 - - - +
128E LEU* 1.3 68.2 + - - +
129E ASP* 3.6 29.4 + - - +
145E THR* 3.5 3.9 - - + +
146E LEU* 3.7 1.4 - - - -
147E ASP* 2.8 67.2 + - + +
156F PHE* 3.7 31.6 - - + -
141G ARG* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA* 5.2 1.2 - - - +
41E ALA* 3.5 25.1 - - + +
126E PHE* 3.9 13.2 - - + -
127E LYS* 1.3 78.2 - - - +
129E ASP* 1.3 73.3 + - - +
130E VAL* 4.1 19.1 - - + -
144E ILE* 4.5 2.2 - - + -
145E THR 3.3 10.1 - - - +
146E LEU* 3.7 21.1 - - + -
156F PHE* 3.4 27.5 - - + -
100G MET* 4.5 5.2 - - - -
104G TYR* 3.9 34.3 - - + -
107G THR* 5.5 2.0 - - + -
108G LEU* 4.2 17.3 - - + -
111G LEU* 5.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ALA* 5.2 2.2 - - - -
127E LYS* 3.6 24.2 + - - +
128E LEU* 1.3 79.3 - - - +
130E VAL* 1.3 70.1 + - - +
131E LYS* 4.3 11.8 - - - +
143E VAL 3.7 0.9 - - - +
144E ILE* 3.3 4.9 - - - +
145E THR* 3.0 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLU* 4.9 2.4 + - - +
128E LEU* 4.1 8.7 - - + -
129E ASP* 1.3 77.6 - - - +
131E LYS* 1.3 62.3 + - - +
142E ALA* 4.8 2.0 - - + -
143E VAL 3.7 2.7 - - - -
144E ILE* 4.0 15.3 - - + -
108G LEU* 3.9 29.4 - - + +
111G LEU* 4.2 22.7 - - + +
112G VAL* 4.8 10.1 - - + -
115G LYS* 3.3 43.5 + - + +
116G PHE* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ASP* 4.1 11.0 - - - +
130E VAL* 1.3 74.5 - - - +
132E LYS* 1.3 70.6 + - - +
133E VAL* 3.8 20.3 + - + -
142E ALA* 3.3 5.5 - - - +
143E VAL* 2.7 49.9 + - + +
115G LYS* 5.6 0.2 - - - +
116G PHE* 4.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E VAL 4.3 0.6 + - - -
131E LYS* 1.3 78.3 - - - +
133E VAL* 1.3 71.8 - - - +
140E GLU* 3.4 27.9 + - + +
141E ARG 3.5 4.9 - - - -
115G LYS* 3.2 37.5 - - + +
116G PHE* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E LYS* 3.8 26.9 + - + -
132E LYS* 1.3 81.3 - - - +
134E ALA* 1.3 68.0 + - - +
140E GLU* 3.3 8.5 - - - +
141E ARG* 2.8 56.4 + - + +
143E VAL* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E VAL* 1.3 84.6 - - - +
135E ASP* 1.3 64.4 + - - +
136E PRO* 3.3 12.7 - - + +
139E GLY 3.8 8.5 - - - +
140E GLU* 5.1 2.2 - - + -
141E ARG* 4.7 1.4 - - - +
----------------------------------------------------------
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