Contacts of the helix formed by residues 110 - 128 (chain A) in PDB entry 6FF8
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 ARG 110 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.8 18.2 + - - +
35A GLY* 3.6 21.0 + - - -
107A ASP* 2.8 47.6 + - - +
108A ILE 3.5 1.0 - - - -
109A SER* 1.3 80.4 - - - +
111A SER* 1.3 60.2 + - - +
112A SER* 3.3 13.1 + - - +
113A THR* 2.7 59.4 + - - +
114A PHE* 3.6 2.1 + - - +
144A LYS* 4.4 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER 4.2 1.6 + - - -
110A ARG* 1.3 69.4 - - - +
112A SER* 1.3 65.8 + - - +
114A PHE* 3.1 13.9 + - - +
115A GLU* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 4.8 1.2 - - - +
110A ARG* 4.0 13.2 + - - +
111A SER* 1.3 80.6 + - - +
113A THR* 1.3 77.2 + - - +
115A GLU* 3.5 14.2 + - - +
116A ALA* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 4.0 21.2 + - + +
36A VAL* 3.7 27.6 - - + -
105A VAL 4.9 0.7 - - - +
106A PHE* 3.5 3.3 - - - +
107A ASP* 3.1 23.0 + - - +
110A ARG* 2.7 51.5 + - + +
112A SER* 1.3 83.9 + - - +
114A PHE* 1.3 63.0 + - - +
116A ALA* 3.6 3.6 + - - +
117A VAL* 3.4 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.7 47.5 - + + +
110A ARG 3.6 1.0 + - - -
111A SER* 3.1 17.1 + - - +
113A THR* 1.3 78.7 + - - +
115A GLU* 1.3 71.4 + - + +
117A VAL* 3.1 30.3 + - + +
118A LEU* 5.3 0.7 - - - +
140A LEU* 4.4 1.8 - - + -
157A GLN* 5.1 7.4 - - - -
161A PHE* 3.6 49.5 - + - -
170A TRP* 4.3 16.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 3.0 27.0 + - - +
112A SER* 3.5 14.2 + - - +
114A PHE* 1.3 81.2 - - + +
116A ALA* 1.3 61.0 + - - +
117A VAL 3.4 0.7 + - - -
118A LEU* 3.6 19.2 + - - +
119A LYS* 4.4 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 3.2 44.2 - - + +
87A ARG* 4.2 7.6 - - - +
112A SER 3.2 12.5 + - - +
113A THR 3.8 2.0 - - - +
114A PHE 3.2 0.8 - - - -
115A GLU* 1.3 75.8 - - - +
117A VAL* 1.3 63.7 + - - +
118A LEU 3.2 0.2 - - - -
119A LYS* 3.0 22.5 + - - +
120A TRP* 3.1 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.1 18.5 - - + +
105A VAL 4.2 8.5 - - - +
106A PHE* 3.7 21.1 - - + -
113A THR 3.4 16.8 + - - +
114A PHE* 3.1 22.7 + - + +
116A ALA* 1.3 76.3 - - - +
118A LEU* 1.3 60.7 + - + +
120A TRP* 3.5 6.7 + - + +
121A LYS* 2.8 30.0 + - - +
140A LEU* 4.0 24.0 - - + -
161A PHE* 4.1 24.9 - - + -
167A PHE* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE 5.3 0.9 - - - +
115A GLU* 3.6 12.7 + - - +
116A ALA 3.2 0.8 - - - -
117A VAL* 1.3 77.2 - - + +
119A LYS* 1.3 60.2 + - + +
121A LYS* 3.9 5.3 - - + +
122A SER* 2.7 40.2 + - - +
161A PHE* 3.5 23.6 - - + -
165A HIS* 3.3 54.3 - - + +
167A PHE* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.6 38.6 - - - +
115A GLU 4.7 2.9 - - - +
116A ALA* 3.0 18.9 + - - +
118A LEU* 1.3 79.2 - - + +
120A TRP* 1.3 62.3 + - - +
122A SER* 4.0 3.8 - - - -
123A ASP* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.7 36.2 - - + +
32A GLY* 3.3 39.5 - - - -
33A GLU* 2.7 24.1 + - - -
82A ILE* 4.2 11.2 - - + -
83A ALA 3.9 14.8 - - - -
84A GLY 3.4 20.9 - - - -
87A ARG* 3.5 43.2 - - + +
92A THR* 4.7 1.1 - - + -
96A TYR* 3.6 25.4 - - - -
104A VAL* 4.3 6.1 - - + -
116A ALA 3.1 25.1 + - - -
117A VAL* 3.7 8.7 - - + +
119A LYS* 1.3 76.6 - - - +
121A LYS* 1.3 57.3 + - - +
123A ASP* 3.2 5.2 + - - +
124A LEU* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.9 3.8 - - + +
117A VAL 2.8 22.3 + - - +
118A LEU* 3.9 7.9 - - + +
119A LYS 3.3 0.2 - - - -
120A TRP* 1.3 73.7 - - - +
122A SER* 1.3 57.4 + - - +
124A LEU* 3.4 17.5 + - + +
125A ASP* 2.6 57.9 + - - +
135A PRO* 5.5 2.4 - - - +
136A ILE 5.6 1.1 + - - -
138A ALA* 3.7 19.5 - - + -
165A HIS* 3.0 25.5 + - + +
166A GLY* 3.3 24.3 + - - -
167A PHE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 2.7 31.5 + - - +
119A LYS* 4.0 5.1 - - - -
121A LYS* 1.3 72.0 - - - +
123A ASP* 1.3 58.0 + - - +
125A ASP* 3.9 3.9 - - - +
126A SER* 3.0 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.7 14.9 - - + +
92A THR* 3.0 20.4 + - - +
96A TYR* 2.6 25.8 + - - +
119A LYS 3.1 15.4 + - - +
120A TRP* 3.2 14.7 + - + +
122A SER* 1.3 75.0 - - - +
124A LEU* 1.3 61.7 + - - +
126A SER* 2.5 22.2 + - - -
127A LYS* 2.8 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.5 32.1 - - + -
31A ILE* 4.4 13.5 - - + -
96A TYR* 3.8 17.7 - - + -
102A ALA* 3.9 20.6 - - + -
104A VAL* 4.7 1.8 - - + -
120A TRP 3.0 15.7 + - - +
121A LYS* 3.5 22.2 - - + +
123A ASP* 1.3 76.4 - - - +
125A ASP* 1.3 69.7 + - - +
127A LYS* 3.1 1.6 + - - -
128A VAL* 3.1 42.2 + - + +
136A ILE* 4.1 15.9 - - + -
138A ALA* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 2.6 50.1 + - - +
122A SER* 4.4 4.0 - - - +
124A LEU* 1.3 88.6 - - - +
126A SER* 1.3 55.5 + - - +
128A VAL 4.4 4.5 - - - +
129A HIS* 2.8 31.3 + - + +
135A PRO* 4.1 28.4 - - + +
136A ILE* 4.8 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 4.4 9.4 + - - -
122A SER 3.0 14.6 + - - -
123A ASP* 2.5 27.0 + - - -
125A ASP* 1.3 76.3 - - - +
127A LYS* 1.3 71.1 + - - +
128A VAL 3.8 0.2 - - - -
129A HIS* 4.1 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASN* 6.0 3.6 - - - +
92A THR* 2.7 31.3 + - - +
93A ARG* 3.7 69.1 + - + +
96A TYR* 3.7 16.1 - - + +
97A LYS* 6.0 0.9 - - - -
123A ASP* 2.8 31.5 + - - +
124A LEU 3.1 1.4 + - - -
126A SER* 1.3 88.8 + - - +
128A VAL* 1.3 64.0 + - - +
129A HIS* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 3.6 39.9 - - + +
97A LYS* 4.6 2.2 - - - -
98A GLU* 4.1 13.2 - - - +
99A ALA* 4.2 10.8 - - + +
124A LEU* 3.1 31.5 + - + +
125A ASP* 4.2 4.0 - - - +
126A SER 3.8 1.2 - - - -
127A LYS* 1.3 81.4 - - - +
129A HIS* 1.3 86.9 + - - +
136A ILE* 4.3 20.1 + - + +
----------------------------------------------------------
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