Contacts of the strand formed by residues 85 - 91 (chain A) 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 GLU 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.7 14.5 - - + -
76A LEU 3.1 15.0 - - - +
77A SER* 4.1 5.5 + - - +
83A HIS* 2.8 29.1 + - + +
84A ASP* 1.3 78.1 - - - +
86A ILE* 1.3 66.5 + - - +
87A ASP* 2.3 44.5 - - - +
105A VAL* 3.3 5.9 - - - +
106A PHE* 2.8 47.1 + - + +
167A MET* 4.1 1.7 - - - +
3D BGC 4.7 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE 4.5 0.2 - - - +
75A TYR* 3.2 4.7 - - - +
76A LEU* 2.9 39.2 + - + +
85A GLU* 1.3 77.6 - - - +
87A ASP* 1.3 60.0 + - - +
88A PHE* 5.8 0.6 - - - -
104A ASN 3.8 3.8 - - - -
105A VAL* 4.8 4.0 - - + +
132A VAL* 4.0 31.7 - - + +
134A TRP* 4.2 12.3 - - + -
139A ILE* 3.6 39.0 - - + -
141A PHE* 3.6 28.5 - - + -
162A PRO* 4.8 2.7 - - + -
167A MET* 3.5 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.2 16.9 - - + +
85A GLU* 2.3 40.7 - - - +
86A ILE* 1.3 74.3 - - - +
88A PHE* 1.3 61.1 + - - +
89A GLU* 3.7 25.1 - - + +
103A THR* 3.1 27.4 - - - -
104A ASN* 3.0 26.0 + - - +
106A PHE* 3.4 22.9 - - - -
141A PHE* 3.4 6.2 - - - -
3D BGC 3.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR 3.9 0.6 - - - +
73A ALA* 3.3 4.7 - - - +
74A PHE* 2.9 63.4 + + + +
75A TYR* 5.0 0.3 - - - +
86A ILE 5.8 0.2 - - - -
87A ASP* 1.3 73.3 - - - +
89A GLU* 1.3 63.2 + - - +
90A PHE* 4.1 11.0 - + + -
101A LEU* 3.7 27.6 - - + -
102A GLN 3.5 3.1 - - - -
103A THR* 4.3 4.0 - - + -
130A TYR* 4.2 13.0 - + + -
131A SER 3.4 33.7 - - - -
132A VAL* 3.7 20.4 - - + -
141A PHE* 4.0 16.6 - + + -
142A LEU 3.8 16.2 - - - -
148A ILE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.0 14.1 - - + +
72A THR 3.5 3.4 - - - -
73A ALA* 4.1 16.4 - - + +
75A TYR* 6.0 0.7 - - + -
87A ASP* 3.7 19.4 - - + +
88A PHE* 1.3 77.1 - - - +
90A PHE* 1.3 62.2 + - - +
91A LEU* 3.6 10.8 + - + +
101A LEU* 4.0 1.3 - - - +
102A GLN* 2.7 56.8 + - + +
104A ASN* 4.6 1.0 - - - +
179A TRP* 3.9 10.4 - - - -
3D BGC 2.6 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 3.7 29.4 - - + -
62A LEU* 3.5 33.7 - - + -
70A THR* 3.6 2.1 + - - +
71A VAL* 3.3 5.9 - - - -
72A THR* 2.7 40.1 + - - +
74A PHE* 5.1 0.9 - - + -
88A PHE* 4.1 13.9 - + + -
89A GLU* 1.3 70.8 - - - +
91A LEU* 1.3 61.7 + - - +
92A GLY 3.8 0.5 + - - -
99A TYR* 3.7 12.3 - + + -
100A ILE 3.4 6.3 - - - -
101A LEU* 3.6 32.3 - - + -
119A LEU* 4.6 7.2 - - + -
123A PRO* 5.4 0.7 - - + -
130A TYR* 3.5 52.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR 3.7 3.6 - - - -
71A VAL* 3.7 15.9 - - + -
89A GLU* 3.8 17.9 - - + +
90A PHE* 1.3 74.5 - - - +
92A GLY* 1.3 65.9 + - - +
99A TYR* 3.2 6.0 - - - -
100A ILE* 2.8 57.2 + - + +
102A GLN* 4.2 4.3 - - + +
116A ARG* 4.0 20.2 - - - +
179A TRP* 3.6 37.9 - - + -
180A ALA* 3.5 27.1 - - - +
1C NAG 3.4 6.6 - - + +
----------------------------------------------------------
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