Contacts of the strand formed by residues 104 - 118 (chain I) in PDB entry 1S9C
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 GLY 104 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ALA* 3.2 2.6 - - - +
22I TYR* 2.9 45.0 + - - -
101I PRO* 5.0 3.4 - - - -
103I ALA* 1.3 77.2 - - - +
105I LYS* 1.3 64.6 + - - -
106I LEU* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I SER* 6.3 1.8 - - - -
20I TYR 3.8 3.6 - - - -
21I ALA* 3.4 24.0 - - + -
104I GLY* 1.3 74.3 - - - -
106I LEU* 1.3 73.5 + - - +
132I SER* 3.9 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I SER* 2.9 30.3 - - - -
20I TYR 3.0 15.5 + - - +
22I TYR* 4.1 14.4 - - + +
64I ILE* 3.5 48.5 - - + -
100I LEU* 5.4 3.6 - - + -
101I PRO* 5.6 5.8 - - + -
104I GLY* 5.0 0.7 - - - -
105I LYS* 1.3 85.9 - - - +
107I LYS* 1.3 62.1 + - - +
108I CYS* 4.6 1.6 - - - -
130I SER* 4.7 5.8 - - - -
131I TYR 3.3 18.2 - - - +
132I SER* 3.6 14.1 - - - +
137I ILE* 3.7 23.6 - - + -
138I CYS* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I PRO* 4.5 14.4 - - + -
18I PHE 3.6 7.6 - - - +
19I SER* 4.3 4.5 - - - -
106I LEU* 1.3 73.7 - - - +
108I CYS* 1.3 64.2 + - - +
109I GLU* 3.2 29.4 + - - +
130I SER* 3.4 0.9 - - - -
131I TYR* 2.8 46.9 + - + +
132I SER 5.0 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I PRO* 3.4 7.1 - - - +
18I PHE* 2.6 78.6 + - + +
20I TYR 4.5 4.0 - - - -
64I ILE* 3.7 17.0 - - - -
65I GLY* 4.6 0.2 - - - -
106I LEU 4.5 7.6 - - - -
107I LYS* 1.3 77.1 - - - +
109I GLU* 1.3 65.2 + - - +
128I VAL* 4.4 3.1 - - + -
129I TYR 3.3 5.6 - - - +
130I SER* 3.4 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LYS* 6.4 2.0 - - + -
15I LEU 4.9 2.9 - - - +
17I PRO* 4.3 16.3 - - + +
107I LYS* 3.2 30.9 + - + +
108I CYS* 1.3 80.7 - - - +
110I ALA* 1.3 63.7 + - - +
111I VAL* 4.5 2.5 - - + +
127I ASP 4.0 0.2 - - - +
128I VAL* 3.2 4.2 - - - -
129I TYR* 2.9 43.0 + - + +
131I TYR* 3.7 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LYS* 3.2 4.3 - - - +
15I LEU* 3.0 51.2 + - + +
16I PRO 5.2 1.0 + - - +
18I PHE* 4.7 5.3 - - + -
68I SER* 3.9 24.7 - - - +
108I CYS 4.3 0.4 - - - -
109I GLU* 1.3 73.0 - - - +
111I VAL* 1.3 74.1 + - - +
126I MET* 4.4 4.9 - - - -
127I ASP 3.5 7.2 - - - +
128I VAL* 4.0 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I GLY* 3.8 19.7 - - - +
14I LYS* 3.5 24.5 - - + +
15I LEU* 4.0 1.3 - - - +
109I GLU* 4.5 7.0 - - + +
110I ALA* 1.3 88.5 - - - +
112I VAL* 1.3 68.8 + - - +
113I ALA* 3.5 11.9 - - + +
126I MET* 2.8 28.1 - - - +
127I ASP* 3.0 18.8 + - + +
129I TYR* 4.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ALA* 3.2 24.2 - - + +
11I ILE 3.0 15.6 - - - +
12I GLY* 3.7 0.6 + - - -
13I GLN 3.8 19.0 + - - +
15I LEU* 4.5 2.7 - - + -
77I ILE* 3.4 37.2 - - + -
80I LEU* 5.8 0.9 - - + -
111I VAL* 1.3 84.2 - - - +
113I ALA* 1.3 51.3 + - - +
114I ASP 2.6 36.1 + - - +
115I VAL* 4.1 8.3 - - + -
124I ILE* 5.0 10.1 - - + -
125I ILE 3.4 5.6 - - - +
126I MET* 4.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE 3.3 9.0 - - - +
12I GLY* 5.4 0.7 - - - -
111I VAL* 3.5 12.4 + - + +
112I VAL* 1.3 71.7 - - - +
114I ASP* 1.3 56.6 + - - +
125I ILE* 2.9 20.7 + - + +
127I ASP* 3.4 28.0 - - + +
160I LYS* 2.7 48.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 3.4 17.3 - - - +
112I VAL* 2.6 19.8 + - - +
113I ALA* 1.3 75.2 - - + +
115I VAL* 1.3 95.0 + - - +
116I LEU* 3.7 3.3 - - + +
125I ILE* 3.4 27.1 + - + -
155I LYS* 3.2 32.7 + - - -
158I SER* 2.8 33.0 + - - +
159I ASP 5.1 0.2 + - - -
160I LYS* 3.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I PHE* 3.8 36.1 - - + +
8I ALA* 5.5 0.9 - - - -
10I ALA* 4.4 10.5 - - + +
11I ILE* 4.2 14.2 - - + +
80I LEU* 5.4 4.9 - - + -
112I VAL* 4.1 14.1 - - + -
114I ASP* 1.3 99.1 + - - +
116I LEU* 1.3 66.0 + - - +
122I VAL* 3.4 24.9 - - + -
123I VAL 3.1 7.6 - - - -
124I ILE* 4.3 13.5 - - + -
152I PHE* 4.2 9.0 - - + -
154I GLY* 5.6 1.2 - - - -
155I LYS* 4.8 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I ASP* 3.7 7.4 - - - +
115I VAL* 1.3 84.2 - - - +
117I ASP* 1.3 62.0 + - - +
118I LYS* 4.6 16.4 - - - +
122I VAL* 2.9 24.0 - - - +
123I VAL* 2.8 34.2 + - + +
125I ILE* 3.9 28.5 - - + -
152I PHE* 4.3 4.3 - - - -
155I LYS* 3.6 20.0 - - + +
156I ARG 4.8 0.9 - - - +
157I THR* 3.3 29.4 - - - +
158I SER* 3.6 17.0 - - - -
161I VAL* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 1.3 76.7 - - - +
118I LYS* 1.3 65.3 + - - +
119I GLY 3.4 6.3 + - - +
121I GLY 3.8 7.4 - - - +
122I VAL* 4.1 0.2 - - - +
151I GLY* 4.4 7.9 + - - +
152I PHE* 3.5 44.1 + - + +
153I GLY* 3.8 1.0 - - - -
154I GLY* 3.3 31.3 + - - +
155I LYS 3.5 15.8 + - - +
156I ARG* 5.2 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 4.2 14.6 - - - +
117I ASP* 1.3 72.8 - - - +
119I GLY* 1.3 52.0 + - - +
120I SER* 2.6 20.4 + - - -
121I GLY 2.8 16.3 + - - +
122I VAL* 4.3 0.2 - - - +
123I VAL* 3.2 33.0 - - + -
145I PHE* 4.0 16.6 - - + -
156I ARG* 2.7 74.7 + - - +
----------------------------------------------------------
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