Contacts of the helix formed by residues 93 - 109 (chain A) in PDB entry 5UM9
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 LYS 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 4.9 2.0 - - + +
90A PRO* 2.9 18.4 + - + +
92A LEU* 1.3 75.8 - - - +
94A SER* 1.3 65.7 + - - +
95A GLY 3.2 2.9 - - - -
96A GLU* 2.9 9.0 + - + -
97A LEU* 2.7 42.7 + - + +
100A ARG* 4.0 13.6 - - - +
158A GLU* 2.9 31.2 + - - +
233A ASP* 3.7 31.9 - - - +
234A TYR* 3.8 20.0 + - + -
5E C 5.4 0.2 + - - -
6E T 3.9 9.3 + - - -
7E T 3.0 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO 3.6 2.8 + - - -
91A GLN* 2.5 26.6 + - - +
92A LEU 4.5 0.2 - - - -
93A LYS* 1.3 76.7 - - - +
95A GLY* 1.3 70.5 + - - +
97A LEU* 2.9 16.4 + - - +
98A ALA* 2.7 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 4.1 5.4 + - - -
93A LYS 3.2 1.2 - - - -
94A SER* 1.3 80.8 + - - +
96A GLU* 1.3 62.3 + - - +
98A ALA* 2.9 17.7 + - - +
99A LYS* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 5.0 0.6 + - - -
93A LYS* 2.9 11.7 + - + +
95A GLY* 1.3 70.8 - - - +
97A LEU* 1.3 64.6 + - - +
99A LYS* 2.9 26.0 + - - +
100A ARG* 3.0 49.6 + - - +
232A SER 5.5 0.9 - - - +
233A ASP* 3.5 47.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
89A PRO* 3.7 31.2 - - + -
90A PRO 4.7 0.9 - - - +
93A LYS* 2.7 47.7 + - + +
94A SER* 3.3 19.1 - - - +
96A GLU* 1.3 72.6 - - - +
98A ALA* 1.3 58.7 + - - +
100A ARG* 4.2 9.6 + - - +
101A SER* 3.7 14.9 + - - -
5E C 4.1 20.9 - - - +
6E T 3.9 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER 2.7 11.0 + - - +
95A GLY* 2.9 11.0 + - - +
97A LEU* 1.3 77.5 - - - +
99A LYS* 1.3 69.1 + - + +
101A SER* 2.9 26.7 + - - -
102A GLU* 3.1 7.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
95A GLY* 3.3 22.9 - - - +
96A GLU* 2.9 17.6 + - - +
98A ALA* 1.3 81.2 - - - +
100A ARG* 1.3 64.8 + - - +
102A GLU* 2.9 31.2 + - - +
103A ARG* 3.2 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY 4.5 1.0 - - - +
93A LYS* 4.0 9.1 - - - +
96A GLU* 3.0 42.7 + - - +
97A LEU* 4.4 8.2 - - - +
99A LYS* 1.3 75.2 - - - +
101A SER* 1.3 59.6 + - - +
103A ARG* 3.5 23.9 - - - +
104A ARG* 3.5 21.6 + - - +
233A ASP* 2.6 31.1 + - - -
6E T 3.4 38.3 + - + +
7E T 2.8 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 3.7 11.7 + - - -
98A ALA* 2.9 18.0 + - - -
100A ARG* 1.3 77.7 - - - +
102A GLU* 1.3 58.3 + - - +
104A ARG* 2.9 19.0 + - - +
105A ALA* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 3.1 7.4 + - - +
99A LYS* 2.9 26.8 + - - +
101A SER* 1.3 76.3 - - - +
103A ARG* 1.3 57.7 + - + +
105A ALA* 2.9 11.0 + - + +
106A GLU* 2.8 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS 3.2 9.6 + - - +
100A ARG* 3.5 25.5 - - - +
101A SER 3.2 0.4 - - - -
102A GLU* 1.3 77.3 - - + +
104A ARG* 1.3 60.0 + - - +
106A GLU* 3.6 12.1 - - - +
107A ALA* 3.4 16.1 - - - +
10D C 4.4 6.3 - - - +
11D A 3.5 26.9 - - - +
7E T 3.6 31.0 + - - +
8E G 3.9 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 5.5 0.6 + - - -
100A ARG 3.5 11.7 + - - +
101A SER* 2.9 20.1 + - - +
103A ARG* 1.3 77.0 - - - +
105A ALA* 1.3 67.6 + - - +
107A ALA* 2.9 16.8 + - - +
108A GLU* 3.0 24.1 + - - +
129A ARG 4.6 6.8 + - - +
130A LEU* 3.7 30.5 + - + +
131A VAL 3.3 26.5 + - - -
132A LYS* 3.5 34.9 - - - +
5E C 5.8 0.8 + - - -
6E T 5.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 2.8 16.0 + - - +
102A GLU* 3.3 16.6 - - + +
104A ARG* 1.3 74.4 - - - +
106A GLU* 1.3 59.5 + - + +
107A ALA 2.9 6.8 + - - -
108A GLU* 3.9 2.8 + - - +
109A LYS* 3.8 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 2.8 46.5 + - + +
103A ARG* 3.6 8.1 - - - +
105A ALA* 1.3 70.8 - - + +
107A ALA* 1.3 55.1 + - - +
109A LYS* 5.7 0.7 - - - -
110A GLN* 2.5 36.9 + - - +
405A SM 3.7 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG 3.4 11.4 - - - +
104A ARG 2.9 8.9 + - - +
105A ALA 2.9 2.0 + - - -
106A GLU* 1.3 81.1 - - - +
108A GLU* 1.3 58.1 + - - +
109A LYS 3.3 1.0 - - - +
110A GLN* 2.9 12.4 + - - +
111A LEU* 2.7 34.8 + - - +
126A PHE* 3.9 11.8 - - + +
129A ARG* 5.1 13.5 - - + +
130A LEU* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 3.0 22.3 + - + +
105A ALA* 4.8 3.0 - - - +
107A ALA* 1.3 74.6 - - - +
109A LYS* 1.3 59.7 + - - +
111A LEU* 2.9 22.6 + - + +
112A GLN* 3.6 18.1 + - + +
130A LEU* 3.7 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.8 14.5 + - - +
106A GLU* 5.7 0.2 - - - -
107A ALA 3.3 0.6 - - - -
108A GLU* 1.3 79.0 - - - +
110A GLN* 1.3 63.3 + - + +
112A GLN* 3.3 37.6 + - - +
113A GLN* 4.1 8.2 + - - +
----------------------------------------------------------
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