Contacts of the strand formed by residues 39 - 47 (chain 8) in PDB entry 4N6V
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 LYS 39 (chain 8).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178 GLN* 3.5 7.6 - - - +
378 VAL* 5.3 5.4 - - + -
388 PHE* 1.3 73.6 - - - +
408 ALA* 1.3 72.4 + - - +
418 VAL* 3.3 20.6 + - - +
578 VAL* 3.7 3.8 - - - +
588 HIS* 2.8 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128 ALA* 3.3 23.4 - - + +
168 THR* 3.9 18.8 - - + +
178 GLN* 2.7 33.3 + - + +
208 ALA* 4.5 4.7 - - + +
388 PHE 4.0 0.4 + - - -
398 LYS* 1.3 79.2 - - - +
418 VAL* 1.3 59.9 + - - +
558 ILE* 3.9 9.9 - - + -
568 LYS 3.7 5.4 - - - -
578 VAL* 4.2 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 PRO* 3.5 6.2 - - - +
128 ALA* 3.0 17.6 + - - -
398 LYS* 3.5 34.8 - - - +
408 ALA* 1.3 75.1 - - - +
428 SER* 1.3 62.5 + - - +
568 LYS* 2.8 48.9 + - + +
588 HIS* 4.2 10.5 - - + -
648 PHE* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 THR* 3.6 18.7 - - - +
108 GLN 3.1 18.2 - - - -
118 PRO* 4.1 1.3 - - - -
128 ALA* 3.5 4.8 - - - +
418 VAL* 1.3 83.2 - - - +
438 PHE* 1.3 65.6 + - - +
558 ILE* 3.6 5.0 - - - +
568 LYS* 2.9 47.9 + - - +
958 LEU* 4.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 ALA 4.1 0.5 - - - +
98 THR* 3.3 2.6 - - - +
108 GLN* 2.9 68.3 + - + +
118 PRO 3.5 19.5 - - - -
128 ALA* 4.0 0.4 - - - -
138 THR* 4.6 10.5 - - + -
168 THR* 3.4 37.9 - - + -
428 SER* 1.3 76.9 - - - +
448 LYS* 1.3 74.4 + - - +
458 SER* 4.6 11.7 - - - -
538 TYR* 4.3 18.8 - + - -
548 PHE 3.0 13.5 - - - +
558 ILE* 4.1 4.9 - - + -
958 LEU* 3.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 ALA* 4.0 19.0 - - - +
98 THR* 3.7 21.5 + - - +
108 GLN* 6.2 0.2 - - - +
438 PHE* 1.3 84.0 - - - +
458 SER* 1.3 64.5 + - - +
528 ASN 4.0 0.2 - - - +
538 TYR* 3.5 1.9 - - - -
548 PHE* 2.8 40.5 + - + +
948 GLU* 5.3 6.3 + - - +
958 LEU* 2.7 34.5 + - + -
968 THR* 4.3 5.4 - - - +
978 TYR* 3.5 44.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438 PHE* 4.3 8.3 - - - -
448 LYS* 1.3 79.0 - - - +
468 GLN* 1.3 62.7 + - - +
478 VAL* 6.0 1.2 - - - +
518 THR* 4.0 8.5 - - - +
528 ASN 3.2 9.0 - - - -
538 TYR* 3.8 26.0 - - - -
978 TYR* 3.6 11.1 + - - -
1018 SO4 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458 SER* 1.3 77.2 - - - +
478 VAL* 1.3 68.9 + - - +
488 VAL* 3.6 8.7 + - + +
518 THR* 3.4 4.6 - - - -
528 ASN* 2.8 63.6 + - + +
548 PHE* 4.0 9.1 - - - -
688 ARG* 5.0 2.6 + - - -
978 TYR* 3.3 44.5 - - + +
1018 SO4 3.5 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458 SER* 6.0 1.1 - - - +
468 GLN* 1.3 74.9 - - - +
488 VAL* 1.3 76.9 + - - +
508 GLY 3.9 7.9 - - - +
518 THR* 4.6 11.2 - - + +
1018 SO4 4.6 12.0 + - - +
----------------------------------------------------------
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