Contacts of the strand formed by residues 118 - 131 (chain B) in PDB entry 1TLY
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 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY 5.0 1.6 - - - +
115B ASN* 3.4 29.6 + - - +
116B LYS 4.1 0.4 + - - -
117B ASP* 1.3 75.1 - - - +
119B ARG* 1.3 67.8 + - - +
152B TYR* 4.2 3.4 - - - -
153B GLY 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 2.7 34.6 + - + -
111B ASP* 2.8 16.2 - - - +
112B MET* 3.2 45.1 - - - +
113B GLY 4.9 1.6 - - - +
118B GLY* 1.3 79.0 - - - +
120B GLN* 1.3 58.7 + - - +
150B GLN* 3.0 47.0 - - + +
152B TYR* 3.1 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.3 4.9 - - - -
109B ILE* 3.6 25.6 - - - +
110B TYR* 3.3 6.5 - - - -
111B ASP* 2.6 44.8 + - + +
119B ARG* 1.3 75.9 - - - +
121B SER* 1.3 63.5 - - - +
122B THR* 3.0 25.2 + - - +
148B GLN* 4.5 0.9 - - - +
150B GLN* 3.0 9.9 - - - +
151B ASN* 4.5 7.0 - - - +
152B TYR* 2.8 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 3.0 23.0 + - - -
109B ILE 3.4 4.3 - - - -
110B TYR* 4.5 7.6 - - - -
120B GLN* 1.3 75.1 - - - +
122B THR* 1.3 60.5 + - - +
148B GLN* 3.1 1.8 + - - -
149B TRP* 3.0 46.5 + - - +
150B GLN* 2.8 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN 4.0 0.5 - - - +
108B TYR* 3.0 6.8 - - - -
109B ILE* 2.7 46.3 + - - -
120B GLN* 3.0 24.6 + - - +
121B SER* 1.3 72.0 - - - +
123B TRP* 1.3 62.9 + - - +
124B TYR* 3.6 20.6 - - + +
146B LYS* 3.3 36.1 - - + -
147B TYR 4.1 1.6 - - - +
148B GLN* 2.6 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 5.5 3.6 - + - -
106B ASN* 2.9 35.5 - - - +
107B ASN 4.0 3.8 - - - -
108B TYR* 3.8 23.0 - + + +
121B SER 4.3 0.4 + - - -
122B THR* 1.3 76.4 - - - +
124B TYR* 1.3 72.3 + - - +
125B MET* 3.2 31.8 - - + +
146B LYS* 3.1 7.0 - - - -
147B TYR* 3.1 34.0 + - + +
149B TRP* 3.9 34.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN* 3.3 3.5 - - - -
107B ASN* 2.7 65.7 + - + +
109B ILE* 3.8 14.1 - - + -
122B THR* 3.6 16.6 - - + +
123B TRP* 1.3 76.9 - - - +
125B MET* 1.3 59.5 + - - +
144B TYR* 3.7 17.3 - - + -
145B ALA 3.4 2.7 - - - -
146B LYS* 3.4 39.2 + - + +
163B TYR* 4.4 4.7 - - - -
164B ARG* 3.4 62.2 + - + -
190B ASP* 3.7 11.5 + - - +
241B GLN* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 4.5 9.2 - - + -
105B ALA 3.4 5.2 - - - -
106B ASN* 3.5 17.5 - - - +
123B TRP* 3.2 64.8 - - + +
124B TYR* 1.3 74.6 - - - +
126B GLY* 1.3 60.1 + - - +
144B TYR* 3.6 4.9 - - - +
145B ALA* 2.8 43.5 + - + +
147B TYR* 4.7 4.0 - - + +
160B TRP* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 3.4 14.8 - - - -
105B ALA* 2.5 43.9 + - - +
125B MET* 1.3 77.2 - - - +
127B LEU* 1.3 55.9 + - - -
143B VAL 3.3 11.7 - - - -
144B TYR* 3.9 0.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
86B ILE* 3.9 20.2 - - + -
102B TRP* 3.5 37.5 - - + -
103B TYR 2.9 25.6 - - - +
104B PHE* 4.9 0.2 - - - +
105B ALA* 4.2 1.6 - - - -
126B GLY* 1.3 73.3 - - - -
128B GLY* 1.3 67.0 + - - +
129B THR* 5.3 0.9 - - + -
141B MET 4.4 0.2 - - - +
142B ASN* 3.6 0.9 - - - -
143B VAL* 3.0 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 4.3 1.1 - - - -
102B TRP* 3.6 3.5 - - - -
103B TYR* 2.7 36.3 + - - +
105B ALA* 3.8 7.1 - - - +
127B LEU* 1.3 81.7 - - - +
129B THR* 1.3 64.7 + - - -
141B MET 3.4 4.9 - - - -
142B ASN* 3.3 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 3.6 8.3 + - - +
99B PHE* 3.8 24.4 - - + +
101B GLU 2.7 22.6 + - - -
102B TRP* 4.0 13.7 - - + -
103B TYR* 4.1 4.3 - - - -
127B LEU* 5.6 1.1 - - + -
128B GLY* 1.3 76.2 - - - -
130B ASP* 1.3 73.3 + - - +
131B ILE* 3.6 19.3 - - + -
140B SER* 3.3 8.7 - - - -
141B MET* 2.8 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 4.2 3.5 + - - -
83B ARG* 3.2 12.7 + - - -
99B PHE* 3.6 1.0 - - - -
100B LYS* 3.0 39.9 + - + +
101B GLU* 3.4 14.3 + - + +
103B TYR* 2.5 35.9 + - + -
129B THR* 1.3 80.9 + - - +
131B ILE* 1.3 62.6 + - - +
139B LEU 3.6 3.4 - - - +
140B SER* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.4 18.8 - - + +
99B PHE* 4.3 18.2 - - + -
100B LYS* 3.9 5.9 + - - +
129B THR* 3.6 26.7 - - + +
130B ASP* 1.3 78.0 - - - +
132B ASP* 1.3 70.8 - - - +
133B THR* 3.6 15.8 + - + -
137B MET 5.4 1.4 - - - +
138B SER* 5.2 1.4 - - - -
139B LEU* 2.7 64.1 + - + +
141B MET* 4.0 18.6 - - + +
----------------------------------------------------------
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