Contacts of the strand formed by residues 136 - 144 (chain B) in PDB entry 5T5W
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 LEU 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.7 37.0 - - + -
125B TYR* 4.2 26.0 - - + -
127B LEU* 4.3 17.7 - - + -
131B MET* 5.2 2.2 - - + -
134B LEU* 3.5 26.9 + - + +
135B ASP* 1.3 81.9 - - - +
137B LYS* 1.3 65.3 + - - +
157B PRO* 4.1 0.3 - - - +
158B HIS* 3.0 41.5 + - + +
180B THR* 4.4 9.0 - - + -
181B ILE 3.8 1.6 - - - -
182B TYR* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 3.3 33.1 + - + +
143A TRP* 5.6 0.6 - - - -
147A ASN* 3.6 22.5 - - - +
125B TYR* 4.6 1.6 - - - -
135B ASP* 2.8 39.3 + - - +
136B LEU* 1.3 81.3 - - - +
138B TYR* 1.3 58.7 + - - +
155B VAL* 3.6 28.5 - - + +
156B THR 3.3 13.5 - - - +
157B PRO* 4.0 22.0 - - + -
158B HIS 4.2 1.1 - - - +
180B THR* 3.3 4.2 - - - +
181B ILE* 2.4 47.8 + - - +
11C SER* 5.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 4.2 4.9 - - + -
110B LEU* 4.2 1.3 - - + -
121B ALA 3.3 18.0 + - - -
123B ALA* 3.6 36.5 + - + -
125B TYR* 3.8 13.9 - - - +
137B LYS* 1.3 75.9 - - - +
139B GLU* 1.3 60.8 + - - +
140B VAL* 3.5 34.2 + - + -
154B PRO 4.3 0.7 - - - +
155B VAL* 3.9 1.2 - - - -
156B THR* 3.0 44.8 + - + -
157B PRO 3.3 25.1 - - - -
158B HIS* 4.2 7.0 - - - -
159B GLY 4.9 0.9 - - - -
160B GLN 2.4 25.6 + - - -
161B PRO* 3.4 3.5 - - - +
162B VAL* 3.6 7.7 + - + +
178B ALA* 4.3 6.3 - - + -
179B ARG 3.0 15.0 - - - +
181B ILE* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU* 5.4 3.9 - - - +
138B TYR* 1.3 72.8 - - - +
140B VAL* 1.3 62.4 + - - +
141B ALA 3.8 0.7 + - - -
152B LEU* 3.4 43.3 - - + +
153B PHE 3.5 20.8 - - - +
154B PRO 5.0 0.9 - - - -
155B VAL* 5.1 8.7 - - + +
178B ALA* 3.2 2.1 - - - -
179B ARG* 2.9 72.9 + - + +
181B ILE* 4.3 15.1 - - + +
189B TYR* 4.9 0.5 - - - -
192B PHE* 3.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.2 8.1 - - + -
121B ALA* 4.4 6.3 - - + -
138B TYR* 3.5 34.0 + - + -
139B GLU* 1.3 74.5 - - - +
141B ALA* 1.3 60.7 + - - +
151B THR 3.4 3.1 - - - +
152B LEU* 3.7 4.1 - - - -
153B PHE* 3.2 45.2 + - + +
154B PRO 5.4 1.0 + - - -
162B VAL* 3.8 17.8 - - + +
164B ILE* 4.4 6.3 - - + -
176B LEU* 3.6 29.4 - - + -
177B SER 3.4 5.8 - - - +
178B ALA* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLU 3.8 1.2 + - - -
140B VAL* 1.3 71.5 - - - +
142B PHE* 1.3 60.3 + - - +
143B TRP* 3.3 21.9 - - + -
150B LYS* 4.8 6.3 - - + -
151B THR 3.4 5.4 - - - +
152B LEU* 4.1 9.6 - - + -
176B LEU* 3.3 6.1 - - - +
177B SER* 2.7 43.5 + - - +
192B PHE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 4.2 15.9 - - + -
141B ALA* 1.3 75.5 - - - +
143B TRP* 1.3 64.3 + - - +
151B THR* 2.8 45.1 + - + +
153B PHE* 3.5 25.6 - + + -
164B ILE* 4.0 23.8 - - + -
165B THR 5.1 2.9 - - - -
166B LEU* 4.3 20.0 - - + -
174B HIS* 3.6 44.6 - + + -
175B CYS 3.8 3.1 - - - -
176B LEU* 3.5 26.0 - - + -
198B PHE* 4.5 0.9 - + - -
200B LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA* 3.3 35.2 - - + -
142B PHE* 1.3 87.7 - - - +
144B LYS* 1.3 83.6 + - - +
145B GLU* 4.8 0.8 - - - +
146B GLY 4.6 5.9 - - - +
147B ALA* 4.5 9.0 - - + -
148B GLY 5.2 3.4 - - - -
149B ASN 3.8 8.3 - - - +
150B LYS* 3.7 28.5 - - + -
174B HIS* 3.6 8.2 - - - +
175B CYS* 2.8 44.2 + - + +
176B LEU 4.3 0.9 - - - -
177B SER* 3.5 23.6 - - - -
195B PRO* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 1.3 89.9 - - - +
145B GLU* 1.3 68.7 + - - +
146B GLY 3.0 1.6 + - - -
147B ALA* 3.1 20.3 + - + +
172B GLU* 4.1 15.0 - - + +
173B HIS 3.7 8.5 - - - +
174B HIS* 3.8 22.8 - - + +
----------------------------------------------------------
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