Contacts of the strand formed by residues 97 - 105 (chain H) in PDB entry 3SDI
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 97 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H THR* 3.8 21.3 - - + +
55H VAL* 4.1 19.3 - - + -
87H LEU* 4.0 27.0 - - + +
95H ILE* 2.8 15.2 + - + +
96H GLY* 1.3 72.8 - - - -
98H TYR* 1.3 61.7 + - - +
99H LEU* 4.2 4.3 - - + -
113H ILE 4.0 1.4 - - - +
114H HIS 3.7 1.9 - - - -
115H ALA* 3.2 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 4.5 0.3 - - - +
45H GLY* 3.2 4.3 - - - -
46H ALA* 2.8 54.8 + - + +
47H GLY* 4.2 7.2 - - - -
52H THR* 4.1 0.4 - - - +
96H GLY* 3.9 12.8 - - - -
97H ALA* 1.3 73.2 - - - +
99H LEU* 1.3 60.0 + - - +
113H ILE 3.4 5.6 - - - +
114H HIS* 4.0 25.8 - + + -
115H ALA* 3.5 37.5 - - + +
116H HIS* 5.1 8.0 + + - -
127H LEU* 4.1 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H HIS* 6.3 0.4 - - + -
43H CYS* 4.4 17.0 - - + -
44H ALA 3.2 8.1 - - - +
45H GLY* 3.7 16.2 - - - +
52H THR* 3.9 22.7 - - + -
55H VAL* 3.9 20.4 - - + -
56H THR* 4.5 6.1 - - - +
83H LEU* 4.0 25.1 - - + -
87H LEU* 4.8 10.1 - - + -
97H ALA* 4.5 4.7 - - + -
98H TYR* 1.3 86.2 - - - +
100H ILE* 1.3 65.3 + - - +
101H VAL* 3.9 1.7 + - + +
112H SER* 3.3 3.6 - - - -
113H ILE* 2.8 46.4 + - + +
127H LEU* 3.6 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 3.8 25.7 - - + +
4H VAL* 4.0 2.5 - - - +
5H GLY* 3.9 13.2 - - - +
14H ILE* 4.2 11.4 - - + +
43H CYS* 3.1 5.6 - - - +
44H ALA* 2.9 34.8 + - + +
99H LEU* 1.3 74.7 - - - +
101H VAL* 1.3 62.1 + - - +
102H ALA 4.2 0.2 + - - -
110H LEU* 3.8 26.5 - - + -
111H PHE 3.4 6.7 - - - +
112H SER* 4.6 2.9 - - - -
125H LEU* 3.8 15.5 - - + +
126H SER* 3.7 35.7 - - - +
127H LEU* 3.8 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.3 10.8 - - + -
41H ILE* 4.1 12.8 - - + -
42H TRP 3.6 8.7 - - - +
43H CYS* 4.0 9.2 - - + -
76H VAL* 4.0 21.5 - - + +
79H ALA* 4.7 6.5 - - + -
80H LEU* 4.2 3.6 - - + +
83H LEU* 4.7 4.7 - - + -
99H LEU* 4.8 2.0 - - + +
100H ILE* 1.3 73.9 - - - +
102H ALA* 1.3 62.9 + - - +
109H HIS 4.1 0.3 - - - +
110H LEU* 3.6 2.4 - - - +
111H PHE* 2.8 53.5 + - + +
113H ILE* 3.8 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.7 24.0 - - + -
14H ILE* 3.3 31.2 - - + -
41H ILE* 3.6 6.1 - - - +
42H TRP 2.9 32.7 + - - +
76H VAL* 4.7 1.1 - - - -
100H ILE 4.2 0.2 - - - -
101H VAL* 1.3 76.8 - - - +
103H GLY* 1.3 58.8 + - - +
109H HIS 3.3 5.6 - - - +
110H LEU* 3.9 4.5 - - + -
178H MET* 3.4 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.6 5.2 - - - +
40H LYS 3.1 14.4 - - - -
41H ILE* 4.2 0.4 - - - -
76H VAL* 3.7 17.4 - - - +
102H ALA* 1.3 75.1 - - - +
104H VAL* 1.3 64.8 + - - +
108H SER* 3.5 1.9 - - - -
109H HIS* 3.0 32.7 + - - +
178H MET* 3.7 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 4.6 0.2 - - + -
40H LYS* 3.1 47.7 + - + +
41H ILE* 4.7 3.8 - - - +
74H PRO 4.8 0.9 - - - +
76H VAL* 4.8 0.7 - - - -
103H GLY* 1.3 79.2 - - - +
105H ASP* 1.3 63.9 + - - +
107H GLY 3.4 5.8 - - - +
108H SER* 4.0 15.9 - - - -
178H MET* 3.3 34.7 - - + +
179H GLU 3.9 21.5 - - - +
180H ILE* 4.0 15.3 - - + +
182H LYS 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H GLU* 5.7 0.2 - - - -
74H PRO 3.4 19.1 - - - +
75H ARG* 3.3 12.4 - - - +
76H VAL* 2.9 25.9 + - + +
77H VAL* 4.6 1.2 + - - +
104H VAL* 1.3 76.5 - - - +
105H PRO* 1.3 77.1 + - - +
106H THR* 2.6 44.3 + - - -
107H GLY* 2.9 17.9 + - - +
109H HIS* 3.4 19.7 + - - -
180H ILE* 5.6 4.0 - - - +
----------------------------------------------------------
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