Contacts of the strand formed by residues 97 - 104 (chain L) 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 VAL 97 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L ALA* 3.6 30.5 - - + +
46L ASN 3.3 7.6 - - - +
47L GLY* 4.7 0.2 - - - -
48L PHE 3.8 7.0 - - - +
51L ASP 4.1 3.1 - - - +
52L GLY* 3.5 32.5 - - - +
55L LEU* 4.0 13.9 - - + -
87L LEU* 4.5 1.6 - - + -
95L TYR* 2.8 29.0 + - + +
96L TYR* 1.3 79.9 - - - +
98L HIS* 1.3 62.3 + - - +
99L THR* 4.0 7.3 + - + +
114L ASP 4.1 0.7 - - - +
115L PRO* 3.3 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302K 3SD 6.3 0.9 - + - -
3L ILE* 3.9 8.3 - - - +
45L ALA* 3.6 0.2 - - - -
46L ASN 2.9 32.4 + - - +
97L VAL* 1.3 71.4 - - - +
99L THR* 1.3 61.2 + - - +
100L ILE* 5.5 0.9 - - + -
113L PHE 4.0 10.4 + - - +
114L ASP* 4.5 2.7 - - + -
115L PRO* 4.1 28.3 - - + +
127L GLY* 4.7 7.9 - - - -
128L GLY* 4.1 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L MET* 4.0 14.6 - - - +
44L SER 3.3 10.6 + - - -
45L ALA* 3.9 10.1 - - - -
55L LEU* 3.9 22.2 - - + -
83L ILE* 4.6 1.0 - - - +
87L LEU* 4.0 11.2 - - + -
97L VAL* 4.1 13.7 - - + +
98L HIS* 1.3 76.9 - - - +
100L ILE* 1.3 67.8 + - - +
101L ILE* 4.6 0.5 - - - +
112L SER* 3.4 2.9 - - - -
113L PHE* 2.8 63.0 + - + +
114L ASP 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L ILE* 3.7 32.3 - - + +
4L LEU 4.7 0.2 - - - +
5L GLY* 4.5 6.5 - - - +
14L LEU* 3.7 23.8 - - + +
43L MET* 3.5 2.4 - - - -
44L SER 2.9 32.4 + - - +
98L HIS* 4.2 1.1 + - + -
99L THR* 1.3 79.9 + - - +
101L ILE* 1.3 74.9 + - - +
102L ALA* 5.4 0.2 - - + -
110L VAL* 4.2 14.1 - - + -
111L TYR 3.4 8.7 - - - +
112L SER* 4.0 13.0 - - - -
125L ARG* 3.6 34.3 - - + +
127L GLY* 4.0 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L LEU* 4.9 0.4 - - - -
41L ILE* 4.4 7.4 - - + -
42L VAL 3.2 9.4 - - - +
43L MET* 3.5 25.4 - - + -
76L ILE* 4.0 21.3 - - + +
79L ALA* 4.0 9.4 - - + -
80L ALA* 3.9 36.3 - - + +
83L ILE* 3.7 18.4 - - + -
99L THR* 4.6 0.7 - - - +
100L ILE* 1.3 84.2 - - - +
102L ALA* 1.3 61.6 + - - +
109L ALA 4.8 0.2 - - - -
110L VAL* 3.5 3.3 - - - -
111L TYR* 2.8 47.9 + - + +
113L PHE* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ALA* 4.1 14.8 - - + -
13L VAL 4.2 7.6 - - - +
14L LEU* 4.1 13.9 - - + +
40L ASN 4.1 0.3 - - - +
41L ILE* 3.6 3.8 - - - -
42L VAL* 3.0 49.6 + - + +
76L ILE* 3.6 5.2 - - - -
100L ILE* 5.4 0.7 - - + -
101L ILE* 1.3 76.6 - - - +
103L GLY* 1.3 58.2 + - - +
109L ALA 3.4 11.2 - - - +
110L VAL* 4.5 4.7 - - + -
178L VAL* 4.5 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ALA* 3.5 9.8 - - - +
40L ASN 3.7 14.4 - - - -
76L ILE* 3.5 10.9 - - - +
102L ALA* 1.3 74.7 - - - +
104L LEU* 1.3 61.1 + - - +
108L GLY* 3.6 1.6 - - - -
109L ALA* 2.8 37.9 + - - +
178L VAL* 4.1 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L ASP 3.3 33.0 - - - +
11L PHE* 3.9 9.4 - - - +
40L ASN* 3.7 18.3 + - - +
73L LYS* 5.6 7.5 + - - +
75L SER* 5.8 0.7 - - - -
76L ILE* 3.7 17.0 + - - +
103L GLY* 1.3 78.3 - - - +
105L ASP* 1.3 69.2 + - - +
106L GLY* 3.7 19.3 - - + -
107L LYS 3.1 10.8 - - - +
178L VAL* 4.0 8.5 - - + +
179L THR 3.5 6.5 - - - -
180L LYS* 3.5 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