Contacts of the strand formed by residues 138 - 144 (chain B) in PDB entry 5NC5
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 MET 138 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.2 7.0 - - - +
137B LEU* 1.3 85.3 - - + +
139B VAL* 1.3 58.7 + - - +
140B VAL* 3.3 29.4 - - + -
291B ILE* 3.0 38.1 + - + +
303B ALA* 4.3 22.0 - - - +
306B ILE* 3.7 29.2 - - + -
307B ARG* 4.6 6.7 - - + +
325B TYR* 3.5 27.8 - - + -
327B TYR* 3.4 20.9 - - - +
328B ASP* 3.9 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.3 11.0 - - + -
138B MET* 1.3 72.7 - - - +
140B VAL* 1.4 64.0 + - - +
141B GLY* 4.5 2.7 - - - +
178B PHE* 3.7 33.0 - - + -
288B GLY* 5.5 0.4 - - - -
289B LEU 3.3 5.6 - - - +
325B TYR* 4.3 1.9 - - - +
326B PRO* 3.5 27.1 - - + +
327B TYR* 3.2 28.5 + - + +
610B PHE* 5.2 6.7 - - + -
1120B PUY 3.6 27.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
138B MET* 3.3 33.6 - - + -
139B VAL* 1.4 67.4 - - - +
141B GLY* 1.3 64.6 + - - +
142B VAL* 4.3 10.0 - - + +
162B MET* 4.9 2.7 - - + -
288B GLY* 2.9 5.0 - - - -
289B LEU* 2.7 46.3 + - + -
291B ILE* 4.1 15.9 - - + -
310B LEU* 4.1 22.7 - - + -
323B ILE* 3.6 28.3 - - + -
324B VAL 3.7 4.3 - - - +
325B TYR* 4.1 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 5.0 0.4 - - - -
140B VAL* 1.3 75.7 - - - +
142B VAL* 1.3 65.1 + - - +
287B SER 3.5 8.5 - - - -
288B GLY* 4.0 0.7 - - - -
323B ILE* 3.7 2.4 - - - -
324B VAL* 2.8 49.7 + - - +
326B PRO* 3.7 4.9 - - - +
610B PHE* 4.2 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 4.3 8.3 - - + +
141B GLY* 1.3 80.3 - - - +
143B ILE* 1.3 64.2 - - - +
154B ILE* 3.6 23.3 - - + +
158B VAL* 3.8 26.5 - - + -
162B MET* 3.9 19.7 - - + -
286B ALA* 3.3 3.3 - - - -
287B SER 2.9 35.0 + - - +
288B GLY* 4.7 3.6 - - - -
289B LEU* 5.8 0.4 - - + -
321B LEU* 3.9 25.4 - - + -
322B LYS 3.6 5.4 - - - +
323B ILE* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 4.9 0.2 - - - -
142B VAL* 1.3 83.2 - - - +
144B ASN* 1.3 61.7 + - - +
145B THR* 3.9 22.0 - - + -
154B ILE* 4.4 2.7 - - - -
281B PHE* 3.6 52.9 - - + -
284B GLN* 4.0 15.7 - - + +
285B PRO 3.6 7.9 - - - +
286B ALA* 3.8 9.6 - - + -
320B GLY 3.3 0.3 - - - +
321B LEU* 3.2 7.6 - - - +
322B LYS* 2.9 50.0 + - + +
324B VAL* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 1.3 77.3 - - - +
145B THR* 1.4 59.9 + - - +
146B ASP* 3.5 3.8 + - - +
147B GLY* 3.2 15.8 + - - -
148B THR* 3.1 26.4 + - - -
149B MET* 3.2 42.8 + - + +
154B ILE* 3.9 18.8 - - + +
284B GLN* 3.7 18.5 - - - +
285B PRO* 3.4 13.1 + - + +
319B SER 3.5 9.3 + - - -
320B GLY 3.1 21.1 - - - -
321B LEU* 3.8 1.2 - - + +
----------------------------------------------------------
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