Contacts of the strand formed by residues 125 - 137 (chain B) in PDB entry 5TIN
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 ASN 125 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TRP 3.4 7.0 - - - +
69B ASN* 2.9 28.3 + - - +
120B ILE* 3.4 4.5 - - - +
121B PHE* 3.0 42.9 + - + +
123B ASN* 3.0 30.7 + - - +
124B GLY* 1.3 79.8 - - - +
126B VAL* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLN 4.4 0.2 - - - -
67B LYS* 3.2 27.2 - - - +
68B TRP* 2.7 57.8 + - + +
70B ASP* 4.5 1.1 - - + -
73B LEU* 3.8 26.0 - - + -
93B ILE* 4.5 2.0 - - + -
118B LEU* 3.7 27.1 - - + -
119B ARG 3.5 2.9 - - - -
120B ILE* 4.3 4.3 - - + -
121B PHE* 4.7 2.7 - - - -
124B GLY 3.8 9.2 - - - +
125B ASN* 1.3 81.8 - - - +
127B LEU* 1.3 65.6 + - - +
128B TYR* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A THR* 4.1 14.8 - - + -
65B ARG* 4.2 23.3 - - + -
66B GLN 3.6 3.4 - - - +
67B LYS* 4.0 31.2 - - + -
117B LEU* 3.8 18.6 - - + +
118B LEU* 3.6 5.4 - - - +
119B ARG* 2.8 70.8 + - + +
121B PHE* 4.2 12.7 - - + -
126B VAL* 1.3 74.3 - - - +
128B TYR* 1.3 66.3 + - - +
129B SER* 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU 3.5 1.7 - - - +
65B ARG* 3.4 1.4 - - - -
66B GLN* 2.8 63.4 + - - +
68B TRP* 3.8 32.8 - + + -
90B LEU* 3.5 39.3 - - + +
95B LYS* 4.0 29.5 - - + +
96B PRO* 5.6 1.3 - - + -
116B LYS* 4.5 7.0 - - + -
117B LEU 3.4 7.4 - - - -
118B LEU* 4.9 0.2 - - - +
126B VAL* 4.5 2.9 - - + -
127B LEU* 1.3 75.5 - - - +
129B SER* 1.3 70.3 + - - +
130B ILE* 3.7 30.3 - - + +
112C THR* 4.8 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.7 7.7 - - - -
204A THR* 5.0 2.7 - - - -
63B PHE* 4.0 8.8 - - - +
64B LEU 3.1 4.4 + - - -
65B ARG* 3.2 35.7 + - - -
116B LYS* 3.3 4.0 - - - +
117B LEU* 2.8 59.6 + - - +
127B LEU* 4.2 1.3 - - - -
128B TYR* 1.3 76.5 - - - +
130B ILE* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 4.2 3.6 - - - -
62B ILE 3.7 0.5 - - - +
63B PHE* 3.5 1.2 - - - -
64B LEU* 2.8 62.4 + - + +
66B GLN* 5.2 0.7 - - - +
108B PHE* 3.4 36.1 - - + -
115B ASN 3.7 10.1 - - - +
116B LYS* 3.5 25.8 - - + -
128B TYR* 3.7 26.9 - - + +
129B SER* 1.3 77.9 + - - +
131B ARG* 1.3 73.4 + - - +
132B LEU* 3.8 9.9 + - + +
112C THR* 4.9 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.5 19.7 - - - +
100A PHE 3.5 12.3 + - - -
101A ALA 3.6 11.9 + - - -
103A GLU* 3.0 46.9 + - - -
159A PHE* 3.7 10.0 - - + -
46B ASN* 4.0 0.8 - - - +
61B ASN* 3.1 25.8 + - - +
62B ILE 3.3 10.8 - - - +
63B PHE* 3.7 20.2 - - + -
108B PHE* 4.1 0.2 - - - -
109B HIS* 3.4 33.2 + - + -
115B ASN* 3.0 49.1 + - + +
130B ILE* 1.3 77.7 - - - +
132B LEU* 1.3 72.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL 3.8 0.5 - - - +
61B ASN* 3.3 6.7 + - - -
62B ILE* 2.9 43.0 + - + +
64B LEU* 4.2 14.6 - - + -
100B PHE* 3.7 33.9 - - + -
107B ASN 3.6 9.6 - - - +
108B PHE* 3.6 28.5 - - + -
109B HIS* 3.9 1.6 - - - -
130B ILE* 4.1 13.0 - - + +
131B ARG* 1.3 83.2 - - - +
133B THR* 1.3 61.3 + - - +
134B LEU* 4.4 9.0 - - + -
111C VAL* 3.8 20.2 - - + -
112C THR* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 4.9 5.3 + - - +
59B ARG* 3.9 34.5 - - + +
60B VAL 3.4 9.9 - - - +
61B ASN* 2.9 12.6 + - + +
105B GLY 4.0 0.4 - - - +
106B ALA* 3.2 5.4 - - - -
107B ASN* 3.0 50.3 + - - +
109B HIS* 2.7 28.6 + - - -
132B LEU* 1.3 71.2 - - - +
134B LEU* 1.3 66.5 + - - +
135B THR* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR 3.7 0.5 - - - +
59B ARG* 3.2 6.8 - - - +
60B VAL* 2.9 48.9 + - + +
62B ILE* 4.0 15.3 - - + -
100B PHE* 3.7 54.7 - - + -
103B GLU* 4.5 3.8 - - + -
105B GLY 3.4 2.7 - - - +
106B ALA* 3.5 26.7 - - + -
132B LEU* 4.4 13.0 - - + -
133B THR* 1.3 80.1 - - - +
135B THR* 1.3 61.3 + - - +
136B LEU* 3.8 18.0 + - + -
154B MET* 4.7 1.1 - - - -
111C VAL* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 3.9 27.4 - - + +
58B TYR 3.3 12.1 - - - +
59B ARG* 3.9 17.7 - - + +
103B GLU* 3.5 3.1 - - - -
104B LYS* 2.7 40.6 + - + -
105B GLY* 2.7 24.6 + - - +
133B THR* 5.6 0.5 - - - +
134B LEU* 1.3 71.8 + - - +
136B LEU* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 3.1 5.2 - - - +
58B TYR* 2.8 69.5 + - + +
60B VAL* 4.0 14.6 - - + -
100B PHE* 4.2 9.9 - - + -
102B ASN* 3.4 23.1 - - - +
103B GLU* 3.7 27.6 - - + +
104B LYS* 4.5 0.9 - - - -
134B LEU* 4.0 14.6 - - + -
135B THR* 1.3 75.2 - - - +
137B SER* 1.3 62.2 + - - +
154B MET* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B MET 3.8 8.1 - - - -
58B TYR* 4.3 3.1 - - - -
102B ASN* 2.9 44.0 + - - +
104B LYS* 3.9 22.5 - - - +
136B LEU* 1.3 73.6 - - - +
138B CYS* 1.3 58.8 - - - +
139B PRO* 3.8 13.7 - - - +
153B ILE* 4.4 4.3 + - - +
47C SER* 6.4 2.5 - - - -
----------------------------------------------------------
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