Contacts of the strand formed by residues 138 - 143 (chain C) in PDB entry 4CYM
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 ALA 138 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ALA* 3.4 12.3 - - + +
104C VAL* 4.7 6.5 - - + -
121C LYS* 3.8 32.1 - - + +
124C LEU* 4.7 3.4 - - + -
136C ILE 3.2 6.4 + - - +
137C PRO* 1.3 72.6 - - - +
139C VAL* 1.3 65.0 + - - +
166C GLY 4.3 5.6 + - - +
167C PHE* 3.5 14.8 - - + -
168C ALA* 2.9 32.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
102C ALA 2.9 7.0 + - - +
103C PHE* 3.4 29.4 - - + +
104C VAL 3.2 20.8 + - - +
138C ALA* 1.3 79.2 - - - +
140C LEU* 1.3 71.0 + - - +
141C LEU* 4.2 1.1 - - + -
167C PHE* 4.1 2.2 - - - -
168C ALA* 4.7 2.5 - - + -
169C GLY 4.0 7.9 - - - +
171C PHE* 3.9 27.1 - - + -
184C ALA* 4.8 0.7 - - + +
187C PHE* 3.8 28.0 - - + -
188C LEU* 3.9 25.8 - - + -
191C LYS* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.4 18.4 - - + +
106C PHE* 3.8 33.0 - - + -
114C PHE* 4.5 5.6 - - + -
117C VAL* 4.4 16.4 - - + -
139C VAL* 1.3 73.5 - - - +
141C LEU* 1.3 67.7 + - - +
142C ALA 4.2 0.2 - - - -
158C VAL* 4.5 7.4 - - + -
161C PHE* 4.1 28.3 - - + -
162C CYS* 4.1 12.1 - - - -
167C PHE* 3.8 25.6 - - + -
169C GLY 3.3 15.3 + - - +
170C TRP* 3.2 27.3 - - + -
171C PHE 3.2 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 6.1 0.2 - - + -
41C ILE* 3.9 31.4 - - + -
103C PHE* 3.9 33.7 - - + -
104C VAL 2.9 13.5 + - - +
105C VAL* 3.6 16.1 - - + +
106C PHE* 3.0 30.4 + - - -
139C VAL* 4.2 4.7 - - + +
140C LEU* 1.3 86.2 - - - +
142C ALA* 1.3 59.4 + - - +
143C ASN 3.3 3.6 + - - -
171C PHE* 3.7 4.5 - - + -
173C THR* 3.9 22.7 - - + +
181C ILE* 6.3 0.4 - - + -
184C ALA* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PHE* 3.5 30.6 - - + -
108C ILE* 3.9 22.4 - - + +
140C LEU* 4.2 0.6 - - - +
141C LEU* 1.3 69.8 - - - +
143C ASN* 1.3 59.5 + - - +
145C CYS* 4.4 3.3 - - - +
170C TRP* 4.5 15.0 - - + -
171C PHE 2.9 14.6 + - - +
172C GLU* 3.4 7.7 - - - +
173C THR* 2.8 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL 3.2 19.5 - - - +
37C GLY* 3.7 4.7 - - - -
41C ILE* 3.9 14.2 - - - +
105C VAL* 4.0 12.3 - - + -
106C PHE 2.9 17.2 + - - +
107C ASP* 3.9 0.2 - - - -
108C ILE* 3.0 22.5 + - - +
141C LEU 3.3 0.4 + - - -
142C ALA* 1.3 74.7 - - - +
144C LYS* 1.3 83.4 + - - +
173C THR* 2.7 32.4 + - - +
175C ALA 3.5 8.5 - - - +
1198C GCP 3.1 33.5 + - - +
----------------------------------------------------------
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