Contacts of the strand formed by residues 113 - 126 (chain I) in PDB entry 3IT8
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 PRO 113 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H HIS* 3.4 30.7 + - + -
75H LEU* 6.0 0.2 - - + -
99H SER* 4.5 0.2 - - - -
65I LYS* 4.6 5.8 - - - -
66I GLY 3.2 7.9 - - - +
67I GLN* 3.0 28.0 - - - +
68I GLY 4.1 1.1 - - - +
112I LYS* 1.3 94.5 - - + +
114I TRP* 1.3 61.2 + - - +
115I TYR* 4.4 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H SER* 3.7 10.8 - - - +
102H GLN* 5.7 8.7 - - + +
64I PHE* 3.8 18.2 - - + -
65I LYS* 3.2 10.2 - - - +
66I GLY* 2.8 53.9 + - - -
68I GLY 3.1 27.4 + - - -
69I CYS* 4.5 2.2 - - - -
70I PRO* 4.8 2.4 - - + +
74I VAL* 5.9 0.4 - - + -
76I LEU* 3.8 23.8 - - + -
100I PRO* 3.7 38.4 - - + -
101I CYS* 3.6 18.8 - - - -
112I LYS 4.8 1.6 - - - -
113I PRO* 1.3 75.2 - - - +
115I TYR* 1.3 72.3 + - - +
116I GLU* 4.1 7.6 - - + +
141I TYR* 3.9 28.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H LEU* 4.1 34.4 - - + +
97H ILE* 3.5 49.7 - - + +
98H LYS* 4.2 7.0 - - - +
99H SER* 3.4 20.4 + - - +
63I LEU* 4.3 6.3 - - + -
64I PHE 3.4 4.3 - - - +
65I LYS* 3.2 35.4 + - + -
113I PRO* 4.4 17.6 - - + +
114I TRP* 1.3 81.5 - - - +
116I GLU* 1.3 75.5 + - - +
117I PRO* 4.2 0.2 - - - +
143I LEU* 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLU* 4.8 1.8 - - - +
98H LYS* 3.8 13.3 - - - +
99H SER* 5.2 1.9 + - - +
116H GLU* 5.0 0.7 - - - +
63I LEU* 3.9 1.5 - - - +
64I PHE* 2.9 40.7 + - + +
76I LEU* 4.3 9.2 - - + -
98I LYS* 3.1 53.2 + - + -
99I SER 5.8 0.4 - - - -
100I PRO* 4.4 17.1 - - + +
114I TRP* 4.1 21.6 - - + +
115I TYR* 1.3 84.8 + - - +
117I PRO* 1.3 64.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G PRO* 5.6 0.2 - - - +
96H ALA* 4.2 23.3 - - + -
97H ILE 3.6 20.4 - - - +
98H LYS* 4.3 18.8 - - + +
118H ILE* 5.3 7.4 - - + -
61I GLN* 4.9 8.3 - - - +
62I VAL 3.4 9.0 - - - +
63I LEU* 4.3 10.1 - - + -
98I LYS* 2.9 33.1 + - - +
115I TYR 4.2 1.6 - - - +
116I GLU* 1.3 81.9 - - - +
118I ILE* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLN* 5.5 0.2 - - - +
117G PRO* 5.1 7.0 - - + -
61I GLN* 3.3 9.0 - - - +
62I VAL* 3.1 36.1 + - + -
64I PHE* 4.0 27.6 - - + -
76I LEU 4.2 10.1 - - - +
78I HIS* 3.7 24.7 + - + +
96I ALA* 3.8 30.1 - - + +
97I ILE 4.7 1.3 - - - -
98I LYS* 3.9 34.8 - - + +
117I PRO* 1.3 79.1 - - - +
119I TYR* 1.3 68.1 + - - +
120I LEU* 4.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLN* 3.3 12.0 + - - -
119G TYR* 3.5 54.6 - + + +
57H LEU* 5.7 2.1 - - - +
119H TYR* 3.5 32.1 + + + +
121H GLY* 3.2 37.3 + - - -
59I TYR* 3.4 17.5 - + + +
60I SER 3.6 10.3 - - - -
61I GLN* 4.0 9.9 - - + +
118I ILE* 1.3 76.3 - - - +
120I LEU* 1.3 95.9 + - - +
121I GLY* 4.5 0.7 - - - -
151I TYR* 3.6 20.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLN* 3.2 18.8 - - - +
119G TYR* 4.8 0.2 - - - -
151G TYR* 4.1 2.2 - - - +
59I TYR* 3.1 6.0 - - - +
60I SER 2.9 35.3 + - - +
78I HIS* 3.5 42.0 - - + +
79I THR* 3.8 4.0 - - - -
80I ILE* 4.1 13.7 - - + +
94I LEU* 3.6 34.5 - - + +
95I SER 4.0 5.2 - - - +
96I ALA* 3.7 18.4 - - + -
118I ILE* 4.2 3.1 - - + -
119I TYR* 1.3 94.8 - - - +
121I GLY* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G TYR* 3.6 1.2 - - - -
119G TYR* 3.2 26.8 + - - -
151G TYR* 3.0 30.4 + - - -
57I LEU* 5.0 1.6 - - - -
58I ILE 3.1 12.8 - - - -
59I TYR* 4.0 4.9 - - - -
94I LEU* 3.6 9.1 - - - +
119I TYR* 4.5 0.7 - - - -
120I LEU* 1.3 75.1 - - - +
122I GLY* 1.3 59.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 4.4 0.7 - - - -
59G TYR* 3.5 18.8 - - - -
57I LEU* 3.6 7.1 - - - +
58I ILE 2.9 30.3 + - - +
94I LEU* 3.7 5.2 - - - +
121I GLY* 1.3 74.6 - - - -
123I VAL* 1.3 64.5 + - - -
124I PHE* 3.5 19.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G VAL* 4.1 25.1 - - + -
14G ALA 5.7 0.2 - - - +
15G HIS* 3.8 18.9 - - + +
36G LEU* 4.2 4.0 - - + +
57G LEU* 5.1 0.4 - - + -
59G TYR* 2.9 25.3 + - + +
154G ILE 5.8 0.2 - - - +
155G ILE* 3.9 31.4 - - + -
55I LEU* 4.1 19.7 - - + -
56I TYR 3.2 12.3 - - - +
57I LEU* 4.3 12.6 - - + -
122I GLY* 1.3 72.6 - - - -
124I PHE* 1.3 77.1 + - - +
157I LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 3.7 16.6 - + - -
34G ASN* 3.6 28.7 - - + -
36G LEU* 4.5 3.1 - - - -
54I GLY 3.5 0.5 - - - +
55I LEU* 3.4 6.6 - - - -
56I TYR* 2.8 41.4 + - - +
58I ILE* 4.0 16.6 - - + -
93I LEU* 3.6 54.3 - - + -
94I LEU* 3.7 21.5 - - + -
122I GLY* 3.5 28.3 - - - -
123I VAL* 1.3 77.3 - - - +
125I GLN* 1.3 62.7 + - - +
126I LEU* 3.6 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ARG* 5.2 15.4 - - - +
7G THR 4.0 3.2 + - - -
8G PRO* 2.7 49.2 + - + +
34G ASN* 5.3 1.0 - - - +
36G LEU* 4.2 23.5 - - + +
53I GLU* 5.5 2.1 - - - +
54I GLY* 3.5 15.7 + - - +
55I LEU* 3.4 16.0 - - + +
82I ARG* 3.9 14.7 + - - -
124I PHE* 1.3 70.3 - - - +
126I LEU* 1.3 82.6 + - - +
160J TYR* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I VAL* 3.6 28.3 - - + -
52I SER 4.0 0.4 - - - +
53I GLU* 3.3 5.2 - - - +
54I GLY 2.8 30.5 + - - -
56I TYR* 3.8 35.7 - - + -
58I ILE* 4.1 7.0 - - + -
82I ARG* 3.8 20.6 - - - +
93I LEU* 5.1 0.9 - - + -
124I PHE* 3.6 19.0 + - + -
125I GLN* 1.3 92.2 + - - +
127I GLU* 1.3 62.7 + - - +
130I ASP* 3.5 14.4 - - + +
132I LEU* 3.8 20.9 - - + -
----------------------------------------------------------
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