Contacts of the strand formed by residues 94 - 101 (chain A) in PDB entry 1SAW
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 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.5 16.4 - - + -
77A VAL 3.7 5.6 - - - +
78A MET* 4.5 3.4 - - + +
79A GLY* 3.8 1.6 - - - -
90A ALA 3.9 4.9 - - - +
91A MET* 3.6 19.9 + - + +
92A ASP 3.3 2.7 - - - +
93A TYR* 1.3 78.6 - - - +
95A GLY* 1.3 61.5 + - - +
96A GLY* 3.4 27.6 - - - +
97A TYR* 4.1 15.0 - - + +
137A LYS* 3.0 35.9 + - + +
173A ILE* 3.3 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 11.8 - - - +
77A VAL 2.9 10.3 + - - -
79A GLY* 3.2 20.1 - - - +
94A VAL* 1.3 72.4 - - - +
96A GLY* 1.3 58.4 + - - +
134A PHE* 3.5 14.1 - - - -
136A PRO* 4.1 1.2 - - - +
137A LYS* 3.2 21.9 + - - +
138A GLU* 4.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL 2.9 24.6 + - - -
94A VAL* 3.4 10.0 - - - +
95A GLY* 1.3 78.9 - - - +
97A TYR* 1.3 73.0 + - - -
134A PHE* 3.5 11.7 - - - -
135A VAL 3.3 12.8 - - - -
137A LYS* 3.6 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.0 20.9 - - + -
75A GLY 3.2 16.8 - - - +
76A VAL* 4.0 24.9 - - + -
77A VAL* 4.0 6.1 - - - -
91A MET* 3.2 29.0 - - + +
94A VAL* 4.1 7.3 - - + +
96A GLY* 1.3 81.8 - - - -
98A ALA* 1.3 63.9 + - - +
134A PHE* 3.7 5.5 - - - -
135A VAL* 2.8 39.9 + - + +
137A LYS* 4.0 22.8 - - + +
140A ILE* 3.7 40.8 + - + -
143A PRO* 3.3 28.1 - - + +
169A ILE* 4.6 1.1 - - + -
209A ILE* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.7 20.6 - - + -
74A LEU* 4.1 4.7 - - - -
75A GLY* 2.7 40.5 + - - -
77A VAL* 4.2 0.6 - - - +
97A TYR* 1.3 76.2 - - - +
99A LEU* 1.3 59.2 + - - +
100A CYS* 3.7 1.1 + - - -
131A VAL* 3.7 27.6 - - + -
132A SER* 3.6 10.5 - - - +
133A ALA 4.0 3.8 - - - +
135A VAL* 5.3 2.5 - - - -
187A ILE* 4.4 5.4 - - + -
209A ILE* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.8 20.2 - - + -
73A GLU 3.5 18.6 - - - +
74A LEU* 4.7 1.3 - - - +
98A ALA* 1.3 71.8 - - - +
100A CYS* 1.3 59.7 + - - +
131A VAL* 3.4 3.8 - - - -
132A SER* 3.0 40.8 + - - +
148A LEU* 4.1 13.9 - - + -
207A ALA* 3.7 14.4 - - + +
208A GLY* 3.2 43.1 - - - +
209A ILE* 4.1 22.8 - - + +
213A VAL* 4.2 9.8 - - + +
215A MET* 3.5 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 2.9 34.6 + - - +
75A GLY* 4.3 0.9 - - - -
98A ALA 3.7 7.2 - - - -
99A LEU* 1.3 81.9 - - - +
101A LEU* 1.3 72.0 + - - +
102A ASP 4.1 0.2 - - - -
129A CYS* 4.1 9.0 - - - -
130A PRO 3.3 7.6 - - - +
131A VAL* 3.9 14.8 - - - -
187A ILE* 3.7 20.0 - - - -
189A LEU* 3.4 42.4 - - + -
215A MET* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.3 13.2 - - + -
70A HIS* 5.5 0.4 - - + -
71A GLU 3.1 9.2 - - - +
72A LEU* 4.0 11.2 - - + -
100A CYS* 1.3 87.7 - - - +
102A ASP* 1.3 59.4 + - - +
103A MET* 3.2 15.8 + - - -
128A SER 3.2 14.7 - - - +
129A CYS* 3.4 6.8 - - - +
130A PRO* 3.2 37.2 + - + +
150A LEU* 3.8 25.4 - - + -
189A LEU* 4.7 0.2 - - - -
205A ILE* 3.9 23.6 - - + -
207A ALA* 4.4 1.8 - - + -
215A MET* 3.6 24.2 - - + -
217A PHE* 4.5 4.7 - - + -
----------------------------------------------------------
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