Contacts of the strand formed by residues 2 - 10 (chain K) in PDB entry 3IT8
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 THR 2 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K ILE* 1.3 77.0 + - - +
3K LEU* 1.3 69.2 + - - +
4K LYS* 4.3 10.1 - - + +
24K HIS 4.4 0.7 - - - +
25K TYR* 3.3 11.6 - - - -
26K ASN* 2.7 55.6 + - - +
97K CYS 3.9 4.5 + - - +
98K TYR* 3.9 11.8 - - - +
107K TYR* 5.5 1.8 - - - +
167K ILE* 3.9 4.3 - - - -
210K PRO* 6.3 0.7 - - - -
211K ASP* 3.9 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 3 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 1.3 75.3 - - - +
4K LYS* 1.3 60.6 + - - +
5K TYR* 4.0 15.9 - - + +
23K ASP* 3.6 24.2 - - - +
24K HIS 3.4 8.5 - - - +
25K TYR* 4.4 2.9 - - + -
96K GLY* 3.1 4.7 - - - -
97K CYS 2.9 33.2 + - - +
107K TYR* 3.5 1.9 + - - -
158K PHE* 4.6 0.7 - - + -
163K CYS* 3.9 21.5 - - - -
166K ALA* 4.2 5.8 - - + -
167K ILE* 3.8 36.3 - - + +
170K TYR* 3.7 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 4 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 4.3 9.2 - - + +
3K LEU* 1.3 73.9 - - - +
5K TYR* 1.3 75.1 + - - +
6K ASN* 4.2 5.4 - - + -
22K TYR 3.6 3.5 - - - +
24K HIS* 2.8 67.2 + - + +
94K ILE* 4.7 4.0 - - + -
95K THR 3.9 1.1 - - - +
107K TYR* 3.6 15.5 - - - +
248K PRO* 3.7 33.0 - - + +
325K NAG 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 5 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LEU* 4.0 14.1 - - + +
4K LYS* 1.3 83.7 - - - +
6K ASN* 1.3 59.7 + - - +
7K TYR* 4.2 9.9 - - + -
21K PHE* 3.9 19.1 - + + -
22K TYR 3.5 2.9 - - - -
23K ASP* 3.2 31.0 - - - -
59K THR* 3.4 15.1 + - - +
60K PRO* 3.7 21.3 - - + +
64K TYR* 3.7 9.4 - + - -
93K LEU 3.4 4.2 - - - +
94K ILE* 3.6 3.1 - - - -
95K THR* 2.7 49.8 + - + +
158K PHE* 3.2 37.0 - + - -
166K ALA* 5.2 0.5 - - - +
170K TYR* 2.7 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 6 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LYS* 5.1 8.1 - - - +
5K TYR* 1.3 73.0 - - - +
7K TYR* 1.3 63.7 + - - +
8K THR* 2.9 12.1 + - - -
20K VAL 3.7 0.7 - - - +
21K PHE* 3.1 7.7 - - - -
22K TYR* 2.9 49.1 + - + +
24K HIS* 5.9 0.7 - - + -
92K SER* 4.1 0.5 + - - -
93K LEU 3.6 2.7 - - - -
94K ILE* 3.4 18.3 - - + +
325K NAG 1.5 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K TYR* 4.3 17.7 - + + -
6K ASN* 1.3 73.7 + - - +
8K THR* 1.3 62.6 + - - +
20K VAL 3.5 4.7 - - - +
21K PHE* 3.4 39.9 - + + -
60K PRO* 5.3 3.3 - - - +
64K TYR* 2.7 37.7 + - + +
66K PHE* 4.5 13.9 - + - -
69K TRP* 3.5 37.9 + + + -
70K TYR 5.6 0.2 - - - -
73K MET* 3.7 20.7 - - - +
92K SER* 3.1 5.5 - - - -
93K LEU* 2.8 56.7 + - + -
95K THR* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 8 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K ASN* 2.9 22.5 + - - -
7K TYR* 1.3 69.4 - - - +
9K VAL* 1.3 68.2 + - - +
10K THR* 4.0 15.9 + - - +
18K ASP 3.7 0.7 - - - +
19K GLY* 3.2 2.3 - - - -
20K VAL* 2.8 54.8 + - + +
73K MET* 4.8 0.4 - - - +
90K SER* 4.3 9.4 - - - +
91K LEU 3.3 6.1 - - - +
92K SER* 2.9 20.7 + - - +
325K NAG 3.4 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K THR* 1.3 75.3 - - - +
10K THR* 1.3 62.5 + - - +
17K TYR* 5.1 5.4 - - + -
18K ASP 2.9 8.3 - - - +
19K GLY* 4.5 0.4 - - - -
70K TYR* 3.9 35.7 - - + +
73K MET* 3.7 42.6 - - + +
74K LYS* 4.4 4.3 - - - +
77K LEU* 3.6 20.6 - - + +
90K SER* 3.2 3.1 - - - -
91K LEU* 3.0 36.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K THR* 4.0 9.9 + - - +
9K VAL* 1.3 76.7 + - - +
11K LEU* 1.3 64.3 + - - +
12K LYS* 3.1 19.9 + - + +
17K TYR* 3.1 11.4 - - - -
18K ASP* 2.8 40.8 + - - +
20K VAL* 5.7 2.3 - - - +
77K LEU* 4.6 0.2 - - - -
89K THR* 3.5 24.7 - - + +
90K SER* 3.5 14.8 - - - +
----------------------------------------------------------
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