Contacts of the strand formed by residues 135 - 141 (chain B) in PDB entry 1N99
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 135 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLY* 6.4 0.4 - - - -
232A LEU 5.6 0.2 - - - -
233A LEU* 4.1 14.4 - - - -
131B SER* 3.2 10.6 + - - -
132B ILE 2.8 32.3 + - - -
133B ASP 3.2 2.0 + - - -
134B ASN* 1.3 81.1 - - - +
136B ILE* 1.3 67.0 + - - +
137B PHE* 4.1 3.4 - - - -
157B GLN* 4.5 5.6 - - - -
166B CYS 5.0 0.7 - - - -
167B ALA* 5.1 3.1 - - - -
169B TRP 4.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.8 35.0 - - + -
130B LYS 3.4 3.4 - - - +
131B SER* 3.8 13.5 - - - +
135B GLY* 1.3 78.9 - - - +
137B PHE* 1.3 65.3 + - - +
157B GLN* 3.4 9.6 - - - +
158B VAL* 2.9 40.9 + - + +
166B CYS* 3.7 38.5 - - + +
169B TRP* 3.6 24.7 - - + +
170B SER 4.2 1.6 - - - +
174B ALA* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.9 19.7 - - + -
129B LEU* 3.3 8.2 - - - -
130B LYS* 2.8 39.7 + - + +
132B ILE* 3.6 54.3 - - + -
133B ASP* 5.6 0.2 - - + -
135B GLY* 4.1 7.9 - - - -
136B ILE* 1.3 80.7 - - - +
138B VAL* 1.3 67.7 + - - +
139B GLN* 3.4 1.1 + - - +
155B GLY* 3.5 25.8 - - - +
156B ASP 3.3 8.5 - - - +
157B GLN* 3.5 31.4 - - + -
158B VAL* 4.7 0.4 - - - +
194B PRO* 4.0 10.3 - - + -
195B PHE* 6.2 1.6 - + - -
270B MSE 4.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.8 22.4 - - + -
128B ARG 3.8 3.4 - - - -
129B LEU* 4.0 9.9 - - + -
137B PHE* 1.3 73.6 - - - +
139B GLN* 1.3 62.5 + - - +
140B LEU 4.0 3.4 - - - +
141B VAL* 3.4 29.2 - - + -
152B LEU* 4.7 10.8 - - + -
153B ARG* 3.4 23.8 - - - +
154B PHE* 3.6 7.2 - - - +
155B GLY* 2.9 25.1 + - - -
156B ASP* 2.9 28.1 + - + +
158B VAL* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 2.7 39.4 + - - +
129B LEU 4.4 0.7 - - - -
130B LYS* 3.8 47.7 + - + +
132B ILE* 5.1 5.4 - - - +
137B PHE* 3.4 1.1 + - - +
138B VAL* 1.3 77.1 - - - +
140B LEU* 1.3 62.9 + - + +
154B PHE* 3.4 34.4 - - - -
247B ILE* 4.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY 3.7 0.7 - - - +
127B LEU* 3.5 5.4 - - - +
128B ARG* 2.9 72.6 + - + +
138B VAL* 3.7 1.6 - - - +
139B GLN* 1.3 82.5 - - - +
141B VAL* 1.3 70.4 + - - +
142B GLN* 3.4 27.5 + - - +
154B PHE* 5.5 2.2 - - - -
247B ILE* 4.5 24.0 - - + +
248B GLY* 5.0 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY 3.3 3.1 - - - -
127B LEU* 4.1 7.2 - - + -
138B VAL* 3.4 28.9 - - + -
140B LEU* 1.3 81.7 - - - +
142B GLN* 1.3 70.4 + - - +
143B ALA 3.6 1.7 + - - -
145B SER* 4.0 1.3 - - - +
147B ALA* 4.0 4.7 - - + -
148B SER* 3.5 39.5 - - - +
152B LEU* 3.6 24.2 - - + +
153B ARG* 4.1 6.1 - - - -
154B PHE* 4.3 2.1 - - - +
245B ASN* 5.4 5.4 + - - -
----------------------------------------------------------
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