Contacts of the strand formed by residues 15 - 22 (chain 1) in PDB entry 3J7Y
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 ASN 15 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141 LYS* 1.3 92.0 - - - +
161 ILE* 1.3 58.6 + - - +
331 LYS* 3.8 44.1 + - + +
341 ARG 3.4 11.8 + - - +
351 ASN* 3.0 26.7 + - - +
641 SER* 4.1 0.2 - - - -
651 LEU* 2.8 45.7 + - + +
2848A A 4.6 5.3 - - - +
2849A G 3.3 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141 LYS 4.1 0.6 + - - -
151 ASN* 1.3 75.1 - - - +
171 LEU* 1.3 77.3 + - - +
181 VAL* 3.6 18.6 + - + +
321 THR 3.7 0.3 - - - +
331 LYS* 3.4 7.5 - - - +
341 ARG* 2.8 43.5 + - - +
361 ARG* 3.6 41.5 - - + +
611 LYS* 3.7 30.5 - - + +
631 ARG 4.2 2.5 - - - +
641 SER* 3.9 20.4 - - - -
651 LEU* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 ILE* 1.3 83.1 - - - +
181 VAL* 1.3 60.8 + - - +
311 ASN* 3.9 25.8 - - + -
321 THR 3.5 20.4 - - - +
331 LYS* 5.3 2.9 - - + -
611 LYS* 3.4 0.2 - - - -
621 ILE* 2.8 48.6 + - + +
631 ARG* 3.1 24.4 + - + +
651 LEU* 4.1 7.7 - - + +
1343 TRP* 3.6 52.9 - - + +
2908A U 4.3 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 ILE* 3.6 17.3 - - + +
171 LEU* 1.3 79.4 - - - +
191 ARG* 1.3 60.7 + - - +
201 MET* 4.3 6.0 - - - +
301 PHE 3.8 0.2 - - - +
311 ASN* 3.4 2.9 - - - -
321 THR* 2.8 57.1 + - - +
341 ARG* 3.9 24.7 - - + +
411 LEU* 5.1 1.6 - - + -
581 GLU* 3.7 36.8 - - + +
601 LYS 3.9 3.4 - - - +
611 LYS* 3.7 14.1 - - + -
621 ILE* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 VAL* 1.3 72.6 - - - +
201 MET* 1.3 65.2 + - - +
211 VAL* 4.4 6.1 - - + -
291 CYS* 3.7 24.9 - - + -
301 PHE 3.5 6.7 - - - +
311 ASN* 4.3 8.0 + - - +
581 GLU* 3.5 4.7 - - - +
591 LYS* 2.9 41.5 + - - +
601 LYS* 3.3 32.7 + - - +
621 ILE* 3.4 36.0 - - + +
2903A U 5.2 1.8 + - - -
2905A A 4.1 18.2 - - - +
2906A C 2.8 53.0 + - - +
2907A U 3.9 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 VAL* 4.3 4.0 - - - +
191 ARG* 1.3 76.9 - - - +
211 VAL* 1.3 62.2 + - - +
291 CYS* 3.4 6.8 - - - -
301 PHE* 2.9 52.4 + - + +
321 THR* 4.0 15.7 - - - +
411 LEU* 3.7 24.9 - - + +
431 LEU* 3.5 41.3 - - + -
561 PHE* 3.4 26.2 - - + +
571 VAL 3.4 4.5 - - - -
581 GLU* 3.6 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191 ARG* 4.4 8.1 - - + -
201 MET* 1.3 75.9 - - - +
221 SER* 1.3 73.8 + - - +
231 GLU* 3.7 4.0 + - - +
261 THR* 6.0 1.1 - - + -
271 GLY 5.6 5.4 - - - +
281 PHE 4.3 3.4 - - - +
291 CYS* 3.9 23.1 - - - -
551 LEU 4.3 0.2 - - - +
561 PHE* 3.3 3.4 - - - -
571 VAL* 2.8 35.9 + - + +
591 LYS* 4.0 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 VAL* 1.3 85.1 - - - +
231 GLU* 1.3 64.8 + - - +
241 ALA 3.4 11.0 - - - -
251 GLY 3.2 8.4 + - - -
261 THR* 4.1 12.3 - - - +
281 PHE 2.8 19.6 + - - -
471 ASP* 3.1 27.8 + - - -
541 VAL* 4.5 0.2 - - - -
551 LEU 3.8 6.1 - - - -
561 PHE* 3.1 25.7 - - - -
----------------------------------------------------------
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