Contacts of the strand formed by residues 93 - 100 (chain A) in PDB entry 5UHE
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 VAL 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.8 7.0 - - - +
89A GLU* 3.5 35.4 - - + +
91A GLU* 4.7 2.2 - - + +
92A PRO* 1.3 79.6 - - - +
94A THR* 1.3 63.7 + - - +
95A MET* 4.2 0.6 + - + -
113A PRO* 4.2 15.9 - - + -
114A ALA 5.4 0.2 - - - +
116A VAL* 3.8 25.6 - - + -
138A LEU 3.8 0.2 - - - +
139A VAL* 3.1 6.5 - - - +
140A VAL* 2.7 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 1.3 76.2 + - - +
95A MET* 1.3 75.3 + - - +
96A TYR* 3.5 32.5 - - + +
111A VAL 4.8 0.2 - - - +
113A PRO* 3.8 16.5 - - - +
137A GLU* 3.7 19.5 + - + +
138A LEU 3.3 6.1 - - - +
139A VAL* 3.9 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.4 11.9 - - + -
85A VAL* 4.8 7.0 - - + -
93A VAL* 5.1 1.1 - - + +
94A THR* 1.3 78.3 - - - +
96A TYR* 1.3 75.0 + - - +
110A ILE* 3.7 24.7 - - + -
111A VAL 3.8 13.5 - - - +
112A PRO* 4.9 2.9 - - - -
113A PRO* 3.9 13.5 - - + -
116A VAL* 4.1 18.8 - - + -
118A VAL* 5.4 4.5 - - + -
137A GLU* 3.7 0.7 - - - -
138A LEU* 2.5 66.2 + - + +
140A VAL* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.5 33.4 - - + +
95A MET* 1.3 88.5 - - - +
97A LEU* 1.3 60.4 + - - +
98A ARG* 4.2 32.3 - - + +
110A ILE* 3.4 6.7 - - - +
111A VAL* 2.8 48.0 + - + +
135A GLU* 6.3 0.2 - - + -
136A VAL 3.6 14.4 - - - -
137A GLU* 4.1 23.9 + - + +
138A LEU* 4.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 1.3 77.7 - - - +
98A ARG* 1.3 67.3 + - - +
99A LYS 4.9 1.1 - - - +
105A VAL* 3.8 24.9 - - + -
106A THR 3.5 24.5 - - - +
109A ASP* 3.6 20.0 - - + +
110A ILE* 3.7 15.7 - - + -
111A VAL* 5.3 1.1 - - - -
125A ILE* 4.4 11.7 - - + -
134A LEU* 3.5 18.1 - - + +
136A VAL* 2.7 67.9 + - + +
138A LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.2 32.0 - - + +
97A LEU* 1.3 83.1 - - - +
99A LYS* 1.3 64.2 + - - +
109A ASP* 4.5 5.6 + - - +
111A VAL* 5.9 1.6 - - - +
133A LYS* 5.6 6.3 - - - +
134A LEU 3.5 3.8 - - - +
135A GLU* 3.7 43.1 + - + +
136A VAL 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.4 1.0 - - + +
98A ARG* 1.3 75.9 - - - +
100A GLN* 1.3 70.1 + - - +
102A PRO 4.3 15.6 + - - -
103A GLY* 4.6 7.5 - - - -
104A GLU 4.0 14.6 + - - -
105A VAL* 3.9 28.5 - - + +
109A ASP* 3.4 39.0 - - + +
128A LEU* 3.3 10.3 - - + +
133A LYS* 4.6 1.6 - - - +
134A LEU* 3.2 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 1.3 86.3 + - - +
101A GLY* 1.3 75.8 + - - +
102A PRO 3.8 5.7 - - - +
128A LEU* 4.8 1.1 - - - +
131A LYS 5.8 2.3 + - - -
132A GLY 3.5 13.7 - - - +
133A LYS* 3.5 36.0 - - + +
----------------------------------------------------------
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