Contacts of the strand formed by residues 37 - 45 (chain A) in PDB entry 1ZSV
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 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.0 6.1 - - - -
36A GLU* 1.3 77.2 - - - +
38A LEU* 1.3 58.0 + - - +
39A LEU* 3.9 24.5 - - + -
71A VAL* 4.0 8.5 - - + -
73A GLU 3.3 9.4 - - - +
74A SER* 3.5 26.0 - - - +
76A ASN* 3.7 14.6 - - + +
79A LEU* 3.7 20.0 - - + +
95A SER 3.8 0.5 - - - +
96A ILE* 3.4 5.5 - - - +
97A SER* 3.0 44.4 + - - +
99A GLY 5.3 0.7 - - - +
102A LEU* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.9 19.3 - - - +
29A LEU* 3.4 33.4 - - + -
32A LEU* 3.9 11.8 - - + +
37A VAL* 1.3 71.8 - - - +
39A LEU* 1.3 61.9 + - - +
71A VAL* 3.6 3.1 - - - -
72A VAL* 3.0 46.1 + - + +
73A GLU* 2.9 30.0 + - + +
94A HIS* 4.1 17.7 - - + -
95A SER 3.6 11.0 - - - +
96A ILE* 4.2 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.9 14.4 - - + -
38A LEU* 1.3 73.1 - - - +
40A GLU* 1.3 59.7 + - - +
41A ALA 4.0 0.3 + - - -
67A GLN* 5.1 2.4 - - - +
69A ALA* 3.8 10.3 - - + -
70A LYS 3.4 4.7 - - - +
71A VAL* 3.6 30.7 - - + +
72A VAL* 4.6 2.0 - - - -
85A VAL* 3.8 16.6 - - + -
87A ALA* 3.8 28.0 - - + -
94A HIS* 3.2 10.1 - - - +
95A SER* 2.8 50.4 + - - +
97A SER* 3.9 10.3 - - - -
102A LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 4.2 0.6 + - - -
39A LEU* 1.3 72.0 - - - +
41A ALA* 1.3 74.5 + - - +
42A LEU* 3.3 10.0 + - + +
69A ALA* 3.1 4.6 - - - -
70A LYS* 2.8 38.3 + - + +
72A VAL* 3.3 33.0 - - + +
93A THR 3.7 2.5 - - - +
94A HIS* 3.2 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 4.0 0.6 + - - -
40A GLU* 1.3 80.4 - - - +
42A LEU* 1.3 61.1 + - - +
44A LEU* 4.3 17.5 - - + -
67A GLN* 3.3 30.7 + - - +
68A VAL 3.8 3.4 - - - +
92A THR 3.6 13.9 - - - +
93A THR* 3.0 23.0 + - - +
329A ALA* 3.3 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 3.8 20.4 - - + +
41A ALA* 1.3 76.1 - - - +
43A PHE* 1.3 82.6 + - + +
68A VAL* 2.8 23.8 + - + +
70A LYS* 4.0 21.5 - - + +
84A ILE* 3.9 28.5 - - + -
115A LEU* 4.5 10.1 - - + -
328A LYS* 3.8 4.3 - - - +
329A ALA* 3.2 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 1.3 94.9 - - + +
44A LEU* 1.3 62.0 + - - +
67A GLN* 3.1 5.7 - - - +
68A VAL* 2.8 39.2 + - + -
114A PRO* 6.3 0.7 - - + -
115A LEU* 4.2 23.6 - - + -
116A SER* 4.0 24.7 - - - -
119A LEU* 3.6 17.4 - - + +
302A ILE* 4.8 6.5 - - + -
326A ILE* 3.7 22.7 - - + -
327A VAL 3.5 2.7 - - - -
328A LYS* 3.8 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 4.3 13.0 - - + -
43A PHE* 1.3 77.7 - - - +
45A THR* 1.3 62.6 + - - +
66A GLN 3.8 7.4 - - - +
67A GLN* 3.6 27.4 - - + +
90A GLY 4.3 0.9 - - - +
91A TRP* 4.3 4.0 - - + -
92A THR 3.6 20.6 - - - +
119A LEU* 4.2 3.4 - - - -
306A PHE* 4.0 20.0 - - + -
309A MET* 3.7 28.7 - - + -
326A ILE* 3.5 2.9 - - - -
327A VAL* 2.8 57.9 + - + +
329A ALA* 4.4 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 1.3 74.6 - - - +
46A VAL* 1.3 64.6 + - - +
47A ASP* 3.1 19.9 + - - +
49A TYR* 5.7 0.2 - - - +
50A MET* 3.4 11.2 - - + +
65A GLY* 5.1 0.3 - - - -
66A GLN* 3.2 40.7 + - + +
91A TRP* 4.5 1.0 + - - -
119A LEU* 4.1 24.0 + - + +
124A MET* 6.3 0.4 - - + -
309A MET* 3.7 8.5 - - - +
324A LYS* 2.7 36.0 + - - -
325A THR 4.1 4.3 - - - -
326A ILE* 4.4 2.2 - - - -
----------------------------------------------------------
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