Contacts of the strand formed by residues 94 - 102 (chain K) in PDB entry 1S5E
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 HIS 94 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K GLN* 3.8 11.7 - - - -
18K HIS* 2.9 32.9 + + - -
47K THR 4.1 3.7 + - - +
48K PHE* 3.4 21.6 - + + +
49K GLN 3.0 22.7 + - - -
87K VAL* 3.4 20.5 - - + +
88K TRP 3.5 6.3 - - - -
89K ASN* 3.7 28.2 + - + +
91K LYS 3.6 13.2 - - - -
92K THR* 5.3 3.1 - - + -
93K PRO* 1.3 72.2 - - + +
95K ALA* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLN* 3.4 11.2 - - + +
51K GLU* 3.6 38.6 - - + +
87K VAL* 3.1 5.6 - - - -
88K TRP* 2.8 47.0 + - + +
91K LYS* 4.2 13.8 - - + +
93K PRO 3.4 1.0 + - - -
94K HIS* 1.3 70.8 - - - +
96K ILE* 1.3 63.8 + - - +
97K ALA 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K ILE* 4.0 11.7 - - + -
48K PHE* 3.8 28.7 - - + -
49K GLN 2.8 22.3 + - - +
50K VAL* 4.4 8.6 - - + +
51K GLU 5.7 0.5 + - - -
68K MET* 4.1 20.6 - - + -
72K LEU* 3.8 27.8 - - + -
85K LEU* 4.3 17.5 - - + -
86K CYS 3.8 4.0 - - - +
87K VAL* 4.3 5.2 - - + -
88K TRP* 3.6 5.4 - - - -
95K ALA* 1.3 73.5 - - - +
97K ALA* 1.3 63.2 + - - +
98K ALA 3.6 25.1 - - - +
31L LEU* 3.4 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K TYR* 6.2 1.3 - - + -
15K THR* 5.2 0.9 - - + -
86K CYS* 2.8 29.5 + - - +
87K VAL* 4.6 1.1 - - - -
88K TRP* 3.5 31.6 - - + -
95K ALA 3.4 0.6 + - - -
96K ILE* 1.3 75.4 - - - +
98K ALA* 1.3 63.5 + - + +
30L SER* 3.5 0.9 + - - -
31L LEU* 2.8 39.9 + - - +
32L ALA* 3.6 9.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 3.7 18.8 - - + -
8K LEU* 4.9 8.5 - - + -
68K MET* 4.2 2.9 - - - -
85K LEU* 3.5 7.4 - - - +
86K CYS* 2.9 37.6 + - + +
96K ILE* 3.6 5.6 - - - +
97K ALA* 1.3 80.5 - - + +
99K ILE* 1.3 60.1 + - - +
28L THR* 5.2 2.2 - - + -
29L GLU 3.2 14.1 - - - +
30L SER* 3.9 13.0 - - - +
32L ALA* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 3.6 3.8 - - - -
24K ILE* 5.4 0.2 - - + -
40K ILE* 6.0 0.7 - - + -
68K MET* 3.8 23.8 - - + -
71K THR* 4.3 14.1 - - + -
72K LEU* 3.9 24.2 - - + -
75K ALA* 5.3 3.8 - - + -
82K VAL* 4.0 21.1 - - + -
84K LYS 3.6 4.9 - - - +
85K LEU* 3.7 19.5 - - + -
98K ALA* 1.3 75.9 - - - +
100K SER* 1.3 74.9 + - - +
101K MET* 4.5 16.2 - - + -
27L TYR* 4.1 1.5 - - + +
28L THR* 3.3 4.6 - - - +
29L GLU* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE* 3.7 14.4 - - - +
82K VAL* 3.8 1.7 - - - -
83K GLU* 2.5 49.9 + - - -
84K LYS* 3.0 26.4 + - - +
99K ILE* 1.3 75.0 - - - +
101K MET* 1.3 67.3 + - - +
26L SER* 6.1 1.8 - - - -
27L TYR 3.4 4.9 - - - -
28L THR* 3.2 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K THR* 4.5 17.0 - - + -
75K ALA* 4.2 16.6 - - + -
80K ALA* 4.1 24.7 - - - -
81K LYS 3.6 17.5 - - - +
82K VAL* 4.2 9.0 - - + -
83K GLU 4.2 0.7 - - - +
99K ILE* 4.5 11.0 - - + -
100K SER* 1.3 80.1 - - - +
102K ALA* 1.3 61.1 + - - +
26L SER* 3.1 5.3 - - - -
27L TYR* 2.9 58.3 + - + +
73L ARG* 5.0 2.5 - - + -
76L TYR* 3.4 25.3 + - + -
77L LEU* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 5.4 0.5 + - - -
81K LYS* 4.1 15.1 + - - +
83K GLU* 4.3 28.4 - - + +
101K MET* 1.3 75.3 - - - +
103K ASN* 1.3 76.9 + - - +
25L PHE* 3.4 17.7 - - + +
26L SER* 3.9 10.3 - - - -
76L TYR* 3.1 10.4 + - - -
----------------------------------------------------------
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