Contacts of the strand formed by residues 127 - 137 (chain H) in PDB entry 4BEI
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 127 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PRO* 4.2 5.6 - - - -
125H ALA 3.7 1.4 + - - -
126H ASP* 1.3 74.5 - - - +
128H LYS* 1.3 62.4 + - - -
129H TYR* 3.5 8.0 - - - -
150H VAL* 3.4 3.3 - - - -
151H LYS 2.8 36.4 + - - -
153H VAL* 4.3 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LYS 4.4 0.3 - - - +
82H GLY* 3.9 2.6 - - - -
83H PRO* 3.5 23.1 - - - +
127H GLY* 1.3 71.2 - - - -
129H TYR* 1.3 61.8 + - - +
130H THR* 5.6 0.2 - - - -
148H GLU* 6.2 4.9 - - + +
149H PHE 3.9 4.0 - - - +
150H VAL* 4.3 11.9 - - + -
153H VAL* 4.9 1.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ILE* 3.8 13.0 - - + -
81H LYS 3.4 3.8 - - - -
82H GLY* 3.6 20.0 - - - -
83H PRO* 3.6 14.5 - - + +
86H ILE* 4.0 6.6 - - + +
88H PHE* 4.1 18.6 - + - -
120H VAL* 4.8 4.3 - - + -
124H MET* 3.4 11.5 - - + +
125H ALA* 2.5 42.5 + - - -
127H GLY 3.5 16.2 - - - -
128H LYS* 1.3 75.2 - - - +
130H THR* 1.3 63.0 + - - +
148H GLU* 3.3 8.7 - - - +
149H PHE* 2.8 74.8 + + + +
151H LYS* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H SER 3.9 0.5 - - - +
80H ILE* 3.5 3.4 - - - -
81H LYS* 2.7 50.2 + - + +
128H LYS 5.6 0.2 - - - -
129H TYR* 1.3 75.3 + - - +
131H VAL* 1.3 70.3 + - - +
132H SER* 4.0 4.1 + - - +
146H ASN* 3.8 27.4 - - + +
147H GLN 3.6 8.1 - - - +
148H GLU* 4.5 13.8 + - + +
1272H O4B 4.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 3.7 20.0 - - + +
46H LEU* 4.3 13.7 - - + -
60H SER* 5.7 0.2 - - - -
78H LEU* 3.8 17.3 - - + -
79H SER 3.6 2.5 - - - -
80H ILE* 3.7 17.7 - - + -
118H PHE* 3.6 22.0 - - + -
129H TYR 4.1 0.2 - - - -
130H THR* 1.3 73.9 - - - +
132H SER* 1.3 62.1 + - - +
146H ASN* 3.2 5.9 - - - +
147H GLN 2.7 39.5 + - - +
149H PHE* 3.3 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ILE* 5.3 5.6 - - - -
78H LEU* 3.7 4.1 - - - -
79H SER* 2.8 39.6 + - - -
130H THR* 5.0 4.5 - - - -
131H VAL* 1.3 74.8 - - - +
133H LEU* 1.3 61.5 + - - +
134H GLN* 2.8 39.5 + - - +
144H LYS* 4.4 2.6 - - - +
146H ASN* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ALA* 4.2 15.3 - - + -
43H ASN 3.2 28.9 - - - +
44H LEU* 3.7 9.9 - - + +
62H LEU* 4.0 25.8 - - + -
63H GLY 3.9 13.0 - - - +
64H ILE* 4.2 9.9 - - + -
76H TYR* 3.9 23.1 - - + -
77H TRP 3.8 9.9 - - - +
78H LEU* 3.7 14.0 - - + +
132H SER* 1.3 71.3 + - - +
134H GLN* 1.3 69.3 + - - +
135H VAL* 4.6 1.1 - - + -
144H LYS* 3.2 7.6 - - - +
145H ALA 2.8 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G GLY 3.0 23.9 + - - -
212G LEU* 3.4 19.1 - - + +
213G ILE* 2.9 33.0 + - - +
76H TYR* 3.2 5.4 - - - +
77H TRP* 3.0 60.9 + - + +
79H SER* 5.0 1.3 - - - -
132H SER* 2.8 39.3 + - - +
133H LEU* 1.3 74.3 - - - +
135H VAL* 1.3 64.0 + - - +
143H PHE 3.6 3.8 - - - -
144H LYS* 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ILE* 4.2 20.4 - - + -
42H ALA* 4.2 14.8 - - + -
64H ILE* 3.9 31.4 - - + -
74H PHE* 3.8 35.2 - - + -
75H LYS 3.5 3.6 - - - +
76H TYR* 4.1 0.7 - - + -
133H LEU* 4.6 3.6 - - + -
134H GLN* 1.3 78.1 - - - +
136H VAL* 1.3 66.5 + - - +
137H ALA 4.5 0.9 - - - +
141H LYS 3.8 1.0 - - - +
142H VAL* 3.5 5.8 - - - +
143H PHE* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G LEU* 4.0 27.6 - - + -
241G SER* 4.0 28.9 + - - +
242G TYR* 4.3 13.5 - - + -
243G PRO* 4.9 0.7 - - + -
74H PHE* 3.4 2.0 - - - -
75H LYS* 2.7 44.1 + - + +
77H TRP* 3.7 27.8 - - + -
135H VAL* 1.3 75.5 - - - +
137H ALA* 1.3 69.7 + - - +
140H GLY 4.7 5.6 - - - +
141H LYS 3.8 5.6 - - - +
142H VAL* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G SER* 3.9 6.0 - - - -
38H PRO 5.4 2.0 - - - +
40H ILE* 4.5 8.7 - - + -
72H VAL* 4.7 7.9 - - + -
73H LYS 4.2 4.3 - - - +
74H PHE* 3.8 12.6 - - + -
135H VAL* 4.0 1.8 - - - +
136H VAL* 1.3 75.6 - - - +
138H GLU* 1.3 56.4 + - - +
139H ASN* 3.0 20.9 - - - +
140H GLY* 2.8 27.9 + - - -
141H LYS 3.1 14.5 + - - +
143H PHE* 4.1 15.5 - - + -
----------------------------------------------------------
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