Contacts of the strand formed by residues 128 - 134 (chain B) in PDB entry 1UMZ
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 HIS 128 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 3.2 7.2 - - - -
60B MET 2.9 30.2 + - - -
121B PHE* 3.2 51.2 - + + +
122B ASP 4.6 2.2 + - - -
123B PRO* 4.8 1.8 - - + -
126B GLU* 3.4 30.1 + - + +
127B PHE* 1.3 77.3 + - - +
129B TYR* 1.3 62.1 + - - +
130B TYR* 3.4 25.3 - - + +
144B ASP* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 3.4 22.2 - - - +
58B MET 3.6 3.4 - - - -
59B GLN* 3.4 41.6 + - + -
128B HIS* 1.3 73.2 - - - +
130B TYR* 1.3 63.6 + - - +
131B SER* 4.2 3.1 - - - -
143B VAL* 3.4 5.2 - - - +
144B ASP* 2.7 54.2 + - - +
201B SER* 3.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 3.4 1.6 - - - -
58B MET 2.8 33.6 + - - +
60B MET* 3.8 32.0 + - + -
62B LEU* 4.5 2.1 - - + +
74B PHE* 3.4 19.7 - - + -
88B PHE* 4.2 15.7 - + + -
90B PHE* 3.5 41.3 - + + -
101B LEU* 4.3 2.2 - - + -
119B LEU* 3.9 1.8 - - + +
121B PHE* 3.5 25.2 - + - -
123B PRO* 3.9 10.0 - - - +
128B HIS* 3.4 28.2 - - + +
129B TYR* 1.3 74.9 - - - +
131B SER* 1.3 60.7 + - - +
142B LEU 3.4 2.9 - - - -
143B VAL* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B HIS* 4.2 13.3 + - - -
56B PHE 3.1 12.3 - - - -
57B SER* 3.5 16.8 - - - -
74B PHE* 4.6 0.4 - - - -
88B PHE* 3.4 9.2 - - - -
129B TYR* 5.3 2.7 - - - -
130B TYR* 1.3 76.7 - - - +
132B VAL* 1.3 63.2 + - - +
133B LEU 4.3 0.2 - - - -
140B VAL 3.7 0.2 - - - +
141B PHE* 3.5 0.9 - - - -
142B LEU* 2.8 59.0 + - - +
144B ASP 4.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 3.7 0.9 - - - +
55B HIS* 3.4 8.1 - - - -
56B PHE* 2.9 47.2 + - + +
74B PHE* 4.8 4.0 - - + -
76B LEU* 4.3 13.0 - - + -
86B ILE* 4.0 33.7 - - + +
88B PHE* 3.6 22.2 - - + -
131B SER* 1.3 77.4 - - - +
133B LEU* 1.3 72.2 - - - +
134B TRP* 4.2 12.6 - - + -
139B ILE* 4.3 4.7 - - + -
140B VAL 3.3 6.7 - - - +
141B PHE* 4.8 2.5 - - + -
142B LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 3.5 12.1 - - - +
55B HIS* 4.0 12.8 - - + -
131B SER 4.3 0.2 - - - -
132B VAL* 1.3 73.5 - - - +
134B TRP* 1.3 60.5 + - - +
135B ASN* 4.2 7.0 - - - +
138B MET* 3.7 9.7 - - + +
139B ILE* 3.2 5.2 - - - -
140B VAL* 2.8 54.2 + - + +
142B LEU* 4.5 7.9 - - + +
223B TRP* 3.9 27.6 - - + -
224B TRP* 3.9 16.8 - - + -
229B PHE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR 3.5 22.7 - - - -
52B LEU* 3.8 20.9 - - + -
53B PHE* 3.3 40.2 - + - +
54B GLY* 2.8 39.7 + - - +
56B PHE* 4.1 14.8 - + + -
76B LEU* 4.1 11.4 - - + -
86B ILE* 4.2 2.0 - - + -
132B VAL* 4.2 13.2 - - + -
133B LEU* 1.3 75.7 - - - +
135B ASN* 1.3 70.7 + - - +
138B MET 3.7 2.0 - - - -
139B ILE* 3.6 22.7 - - + -
161B PHE* 4.3 0.2 - + - -
162B PRO* 2.8 35.0 + - + +
165B GLN 4.2 1.3 - - - -
167B MET* 3.4 42.6 - - + -
224B TRP* 4.2 1.7 - - - -
----------------------------------------------------------
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