Contacts of the strand formed by residues 138 - 144 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PHE* 3.4 3.9 - - - +
137C LEU* 1.3 95.3 - - + +
139C VAL* 1.3 69.0 + - - +
140C VAL* 3.9 24.2 - - + -
291C ILE* 3.0 39.8 + - + +
303C ALA* 3.6 41.1 - - + +
306C ILE* 4.0 17.9 - - + -
307C ARG* 5.8 4.7 - - + +
325C TYR* 5.6 7.4 - - - -
327C TYR* 3.2 19.7 - - - +
328C ASP* 4.1 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PHE* 4.6 4.3 - - + -
138C MET* 1.3 81.5 - - - +
140C VAL* 1.3 65.7 + - - +
178C PHE* 3.8 26.5 - - + -
289C LEU 3.1 6.5 - - - +
290C GLY* 4.4 3.8 - - - -
325C TYR* 4.4 3.1 - - - +
326C PRO* 3.1 34.7 - - + +
327C TYR* 3.1 26.3 + - + +
610C PHE* 4.1 16.2 - - + -
628C PHE* 3.8 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C MET* 3.9 28.0 - - + -
139C VAL* 1.3 76.1 - - - +
141C GLY* 1.3 61.7 + - - +
142C VAL* 4.4 4.4 - - + +
162C MET* 5.6 0.9 - - + -
288C GLY* 2.9 3.7 - - - -
289C LEU* 2.7 50.0 + - + +
291C ILE* 4.2 14.1 - - + -
306C ILE* 4.5 8.1 - - + -
310C LEU* 4.2 22.0 - - + -
323C ILE* 3.6 28.9 - - + -
324C VAL 4.1 2.7 - - - +
325C TYR* 4.8 7.4 - - + -
326C PRO* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 1.3 71.3 - - - +
142C VAL* 1.3 65.6 + - - +
287C SER 3.4 8.7 - - - -
288C GLY* 4.0 1.1 - - - -
323C ILE* 3.4 8.8 - - - +
324C VAL* 2.9 50.3 + - - +
326C PRO* 3.6 5.8 - - - +
610C PHE* 4.0 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.4 9.2 - - + +
141C GLY* 1.3 78.1 - - - +
143C ILE* 1.3 67.8 + - - +
154C ILE* 3.6 23.0 - - + +
158C VAL* 3.5 26.9 - - + -
162C MET* 4.6 5.6 - - + -
286C ALA* 3.5 0.7 - - - -
287C SER 2.7 41.8 + - - +
288C GLY* 4.4 3.4 - - - -
289C LEU* 5.9 1.8 - - + -
321C LEU* 3.8 25.1 - - + -
322C LYS 3.4 9.9 - - - +
323C ILE* 4.2 15.5 - - + -
324C VAL* 4.2 0.2 - - - +
610C PHE* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C VAL* 1.3 76.1 - - - +
144C ASN* 1.3 57.7 + - - +
145C THR* 4.1 18.2 - - + -
154C ILE* 4.0 9.2 - - - -
281C PHE* 4.2 23.1 - - + -
284C GLN* 4.4 23.1 - - + +
285C PRO 3.6 17.5 - - - +
286C ALA* 3.8 11.7 - - + -
320C GLY 4.3 0.2 - - - -
321C LEU* 3.5 7.9 - - - +
322C LYS* 2.8 51.6 + - + +
324C VAL* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 1.3 74.3 - - - +
145C THR* 1.3 62.6 + - - +
146C ASP* 3.4 2.8 + - - +
147C GLY* 2.9 33.4 + - - -
148C THR 3.0 10.6 + - - -
149C MET* 3.4 35.7 + - + +
154C ILE* 3.7 21.1 - - + +
284C GLN* 3.5 16.5 + - - +
285C PRO 4.9 1.2 + - - -
319C SER 3.2 13.5 + - - -
320C GLY* 3.1 25.5 - - - -
321C LEU* 3.6 1.8 - - + +
----------------------------------------------------------
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