Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 3SRG
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 VAL 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.3 36.3 - - + -
64A PHE* 4.5 7.2 - - + -
119A THR* 4.8 1.8 - - - -
120A PHE 3.7 4.7 - - - +
121A ILE* 4.4 16.6 - - + +
125A ASN 3.9 9.9 - - - +
126A THR* 1.3 73.3 - - - +
128A TYR* 1.3 73.0 + - - +
145A LYS* 3.6 4.9 - - - +
146A PHE* 2.8 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 3.2 8.3 - - - -
120A PHE* 2.8 50.4 + + + +
122A ASP* 4.0 15.8 + - + -
124A ASP* 5.5 1.4 + - - -
126A THR* 3.7 35.2 - - + +
127A VAL* 1.3 77.2 - - - +
129A LEU* 1.3 58.5 + - - +
130A LEU* 4.2 15.0 - - + -
143A VAL* 4.3 5.8 - - + -
144A PHE 3.3 15.5 - - - +
145A LYS* 4.5 5.3 - - + +
156A LEU* 3.6 28.3 - - + -
175A PRO* 3.9 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.1 24.0 - - + -
85A ILE* 3.9 24.2 - - + -
117A ILE* 4.3 17.3 - - + -
118A SER 3.6 14.4 - - - +
119A THR* 3.8 17.5 - - + -
127A VAL 4.1 1.2 + - - -
128A TYR* 1.3 73.2 - - - +
130A LEU* 1.4 61.1 + - - +
131A VAL* 3.7 22.4 - - + -
143A VAL* 3.7 1.0 - - - -
144A PHE* 2.8 42.5 + - + +
146A PHE* 5.6 1.1 - - + -
153A LEU* 3.9 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.1 8.1 - - - +
118A SER* 2.9 36.7 + - - +
120A PHE 4.9 0.4 - - - +
128A TYR* 4.2 17.5 - - + +
129A LEU* 1.4 76.7 - - - +
131A VAL* 1.3 61.0 + - - +
141A VAL* 4.2 9.4 - - + -
142A GLU 3.3 3.8 - - - +
143A VAL* 4.2 15.9 - - + -
170A ILE* 3.7 15.7 - - + +
172A ALA* 4.0 27.6 - - + -
174A GLY 4.6 5.8 - - - +
175A PRO 4.1 20.6 - - - +
176A GLU* 4.7 1.3 - - - -
178A PHE* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.0 12.1 - - + -
112A PHE* 3.9 12.3 - - + -
114A PRO* 3.6 24.7 - - + -
116A GLY 3.6 3.4 - - - +
117A ILE* 4.1 9.0 - - + -
129A LEU* 3.7 24.9 - - + -
130A LEU* 1.3 81.0 - - - +
132A VAL* 1.3 77.1 + - - +
133A ASN 3.5 0.9 + - - -
141A VAL* 4.3 2.2 - - - -
142A GLU* 2.8 39.5 + - + +
144A PHE* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PRO* 3.3 5.0 - - - +
115A HIS* 2.9 30.2 + - + -
116A GLY 2.9 29.5 + - - +
130A LEU 4.2 0.6 - - - -
131A VAL* 1.3 72.4 - - - +
133A ASN* 1.3 62.6 + - - +
134A HIS* 3.6 17.5 - - + +
140A THR 3.5 7.0 - - - +
141A VAL* 4.4 2.0 - - + +
167A VAL* 3.5 53.2 - - + +
168A ASN 3.8 11.9 - - - +
169A ASP* 4.0 1.8 - - - -
170A ILE* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.0 6.9 - - - +
108A ASP 5.6 1.0 + - - -
111A SER 5.4 0.2 - - - -
112A PHE* 3.6 25.0 - - + +
113A ASN 2.7 33.3 + - - +
132A VAL* 1.3 78.5 - - - +
134A HIS* 1.3 66.7 + - - +
135A PRO* 3.3 23.4 - - - +
139A SER* 3.4 5.2 - - - -
140A THR* 2.8 41.4 + - - +
142A GLU* 3.0 34.5 + - + -
----------------------------------------------------------
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