Contacts of the strand formed by residues 57 - 62 (chain A) in PDB entry 3N9Z
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 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 3.7 1.9 - - - +
53A LYS* 3.4 1.7 - - - -
54A LEU* 2.8 39.8 + - + +
56A ASN* 1.3 92.8 - - - +
58A GLU* 1.3 61.6 + - - +
59A SER* 3.9 18.6 + - - +
82A PHE* 3.7 37.7 - - + -
85A PRO* 6.1 2.0 - - + -
210A ASN* 5.6 6.5 - - - +
358A TYR* 5.6 2.5 - - - +
375A LEU* 4.1 7.0 - - + -
377A GLN* 5.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.9 29.3 - - + -
17A ASP* 4.4 5.2 - - - +
51A ARG* 3.8 23.0 + - + +
52A GLU 3.7 9.0 - - - +
53A LYS* 3.8 31.7 + - + +
56A ASN 3.8 3.6 + - - +
57A VAL* 1.3 74.4 - - - +
59A SER* 1.3 76.0 + - - +
374A THR* 5.4 4.0 - - + +
375A LEU* 3.8 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.2 6.0 - - - +
52A GLU 3.0 32.0 + - - -
57A VAL* 3.9 5.4 + - - +
58A GLU* 1.3 81.4 + - - +
60A VAL* 1.3 62.3 + - - +
61A TYR* 3.8 18.6 + - - -
374A THR* 5.3 1.6 - - - -
375A LEU* 3.3 21.6 - - - +
377A GLN* 2.9 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.4 33.7 - - + -
12A ILE* 4.3 7.4 - - + -
49A ILE* 3.7 30.5 - - + -
50A TYR 3.3 8.1 - - - +
51A ARG* 4.3 3.8 - - + -
59A SER* 1.3 75.3 - - - +
61A TYR* 1.3 61.2 + - - +
62A VAL* 4.5 4.9 - - + -
370A ILE* 4.1 16.8 - - + -
374A THR* 3.9 11.7 - - + -
375A LEU 2.9 10.3 + - - +
376A VAL* 3.4 12.2 - - + +
377A GLN* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 6.5 0.2 - + - -
39A HIS* 3.7 31.7 + + - -
43A PHE* 3.8 9.6 - + + -
49A ILE* 3.3 8.0 - - - +
50A TYR* 2.7 79.5 + + + +
52A GLU* 4.1 16.8 + - + -
54A LEU* 4.5 16.8 - - - +
59A SER* 3.8 27.2 + - - -
60A VAL* 1.3 75.7 - - - +
62A VAL* 1.3 64.8 + - - +
354A THR* 4.7 2.2 - - + -
377A GLN* 3.4 42.4 + - + -
379A ALA* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.7 6.3 - - - -
48A PRO 3.8 5.8 - - - +
49A ILE* 4.1 18.4 - - + -
60A VAL* 4.5 4.5 - - + -
61A TYR* 1.3 78.4 - - - +
63A ILE* 1.3 61.2 + - - +
67A ASP* 4.4 21.1 - - + +
68A VAL* 4.5 10.5 - - + +
71A LEU* 5.2 1.3 - - + -
365A LEU* 4.0 25.1 - - + -
376A VAL* 4.4 9.6 - - + -
377A GLN 2.9 17.4 + - - +
378A VAL* 3.5 22.4 - - + +
379A ALA 2.9 25.8 + - - -
----------------------------------------------------------
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