Contacts of the strand formed by residues 115 - 120 (chain A) in PDB entry 3SE3
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 ILE 115 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.3 19.1 - - + -
109A GLU 3.8 8.7 - - - +
110A ALA* 4.5 4.5 - - - -
114A ALA* 1.3 78.4 - - - +
116A VAL* 1.3 78.0 + - - +
117A ILE* 4.1 8.5 - - + +
142A ILE* 5.1 7.6 - - + -
161A LYS* 3.3 2.2 - - - -
162A ILE* 2.6 48.6 + - + +
165A LEU* 3.9 9.1 - - + +
171A TYR* 4.3 20.6 - - + -
194A ILE* 3.5 28.9 - - + -
196A THR* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A HIS 3.4 0.9 - - - +
108A LEU* 3.2 10.7 - - - +
109A GLU* 2.9 48.2 + - + +
111A GLU* 5.2 3.4 - - - +
115A ILE* 1.3 75.2 - - - +
117A ILE* 1.3 66.6 + - - +
118A HIS* 3.2 34.0 - - + +
159A ARG* 6.1 0.2 - - + -
160A HIS 3.6 8.3 - - - +
161A LYS* 3.5 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 5.1 5.2 - - + -
107A HIS 3.5 3.8 - - - +
108A LEU* 4.0 15.9 - - + -
115A ILE* 4.1 9.6 - - + +
116A VAL* 1.3 75.5 - - - +
118A HIS* 1.3 63.7 + - - +
119A ILE* 3.4 35.0 - - + -
140A LEU* 5.3 10.5 - - + -
156A ILE* 5.0 2.7 - - + -
159A ARG* 3.0 8.0 - - - +
160A HIS* 2.6 62.5 + - + +
162A ILE* 3.7 35.7 - - + -
173A LEU* 5.7 3.8 - - + -
175A VAL* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.7 1.6 - - - -
107A HIS* 2.8 62.3 + - + +
108A LEU 5.2 0.9 - - - -
109A GLU* 4.6 16.5 + - - +
116A VAL* 3.2 31.9 - - + +
117A ILE* 1.3 73.2 - - - +
119A ILE* 1.3 59.1 + - - +
159A ARG* 3.2 37.0 + - + +
248A TYR* 5.7 8.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 3.8 8.5 - - + -
105A GLU 3.1 14.8 - - - +
106A VAL* 4.9 5.8 - - + -
107A HIS* 5.4 1.1 - - - -
117A ILE* 3.4 27.1 - - + -
118A HIS* 1.3 73.9 - - - +
120A SER* 1.3 64.7 + - - +
138A TYR* 3.0 42.0 + - + -
156A ILE* 3.7 25.6 - - + -
158A SER* 3.0 25.4 + - - +
159A ARG* 3.7 2.6 - - - +
175A VAL* 4.1 11.7 - - + -
243A PRO* 3.0 27.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 4.4 0.7 - - - -
105A GLU* 2.6 64.5 + - - +
107A HIS* 5.2 2.7 + - - -
119A ILE* 1.3 78.0 - - - +
121A PRO* 1.3 75.0 + - - +
124A LYS* 5.2 6.1 - - - +
138A TYR* 3.9 6.3 - - - -
243A PRO* 4.8 7.9 - - - -
244A GLY* 5.8 3.4 - - - -
----------------------------------------------------------
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