Contacts of the strand formed by residues 28 - 38 (chain A) in PDB entry 5MWF
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 GLY 28 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 1.3 74.7 - - - +
29A TYR* 1.3 71.8 + - - -
133A PRO* 3.5 0.3 - - - +
134A PHE* 3.0 46.0 + - - +
197A ARG 3.3 13.0 - - - -
198A CYS* 4.0 1.3 - - - -
199A ASP* 3.1 11.1 + - - +
207A CYS* 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 5.8 1.2 - - + +
28A GLY* 1.3 78.6 - - - -
30A PHE* 1.3 61.0 + - - +
31A GLU* 4.1 3.0 - - + +
131A VAL* 4.1 20.4 - - + -
132A ILE 3.7 4.0 - - - -
133A PRO* 3.5 27.1 - - + -
134A PHE* 3.4 7.0 - - - -
196A VAL* 3.3 10.6 - - - +
197A ARG* 2.9 71.0 + - - +
198A CYS 4.8 1.1 - - - -
199A ASP* 2.6 40.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 1.3 72.8 - - - +
31A GLU* 1.3 69.6 + - - +
32A LEU* 4.2 15.5 - - + -
73A VAL* 5.0 2.9 - - + -
75A LEU* 3.8 46.9 - - + -
130A VAL* 3.6 1.1 - - + +
131A VAL* 3.4 4.2 - - - +
132A ILE* 2.8 54.7 + - + +
134A PHE* 3.9 6.3 - - + -
138A TRP* 4.0 7.6 - + - -
142A PHE* 4.4 10.3 - + - -
144A LEU* 4.4 14.4 - - + -
172A ILE* 5.2 0.7 - - + -
194A ILE* 4.0 35.7 - - + -
195A ARG 3.8 3.1 - - - -
196A VAL* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 4.7 5.4 - - + +
30A PHE* 1.3 80.5 - - - +
32A LEU* 1.3 59.7 + - - +
116A ARG* 6.2 0.2 - - - -
129A LEU* 4.6 9.6 - - + +
130A VAL 3.3 5.4 - - - +
131A VAL* 4.2 20.3 - - + +
178A TRP* 3.4 19.9 - - + -
194A ILE* 3.2 7.8 - - - +
195A ARG* 2.5 75.9 + - + +
197A ARG* 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.2 7.0 - - + -
31A GLU* 1.3 76.3 - - - +
33A GLN* 1.3 69.3 + - - +
34A LEU* 4.3 9.6 - - + +
71A VAL* 5.2 5.8 - - + -
73A VAL* 4.3 22.9 - - + -
128A GLY 3.7 1.2 - - - +
129A LEU* 3.5 6.2 - - - +
130A VAL* 2.9 46.2 + - + +
144A LEU* 3.8 29.4 - - + -
146A VAL* 4.2 11.2 - - + -
178A TRP* 4.4 0.2 - - - -
192A LEU* 4.1 17.7 - - + -
193A GLN 3.4 4.7 - - - +
194A ILE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 1.3 73.6 - - - +
34A LEU* 1.3 82.3 + - - +
35A SER 3.9 0.3 + - - -
105A LEU* 5.0 2.2 - - - +
106A PRO* 3.4 21.7 + - - +
107A PRO 5.1 0.2 - - - -
108A ALA* 3.8 30.4 - - + +
116A ARG* 5.1 1.9 + - - -
126A ASP* 3.8 18.7 + - - +
128A GLY* 3.6 13.5 + - - -
129A LEU* 3.6 25.8 - - - +
178A TRP* 4.1 6.7 - - + -
192A LEU* 3.1 7.5 - - - -
193A GLN* 2.7 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.2 9.0 - - + +
33A GLN* 1.3 87.7 + - - +
35A SER* 1.3 60.0 + - - +
36A ALA 4.1 13.9 - - - +
37A LEU* 4.8 5.4 - - + -
71A VAL* 3.9 22.2 - - + -
95A THR* 6.3 1.1 - - + -
98A LEU* 3.6 29.6 - - + -
103A PHE* 4.2 19.3 - - + -
105A LEU* 3.4 15.1 - - - +
128A GLY* 3.1 15.1 + - - +
146A VAL* 5.5 1.1 - - + -
190A LEU* 4.1 24.7 - - + -
191A GLU 3.7 14.1 - - - +
192A LEU* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 3.9 0.4 + - - -
34A LEU* 1.3 74.8 - - - +
36A ALA* 1.3 63.6 + - - +
104A TYR* 3.4 4.7 - - - +
105A LEU* 2.7 48.8 + - - +
106A PRO 4.1 0.7 - - - -
107A PRO* 3.8 25.2 - - - +
191A GLU* 3.1 14.0 + - - +
193A GLN* 3.4 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.9 9.7 - - - +
35A SER* 1.3 82.0 - - - +
37A LEU* 1.3 62.5 + - - +
103A PHE* 3.7 8.0 - - - -
104A TYR* 4.3 20.6 - - + -
189A HIS 4.4 0.4 - - - -
190A LEU* 3.5 3.7 - - - -
191A GLU* 3.0 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.8 9.6 - - + -
36A ALA* 1.3 75.2 - - - +
38A ARG* 1.3 69.9 + - - +
39A ASN* 4.3 7.2 - - + +
69A THR* 4.2 18.6 - - + +
71A VAL* 5.0 2.0 - - + -
101A ASN 3.7 18.8 - - - +
102A SER* 3.3 3.8 - - - -
103A PHE* 3.1 58.4 + - + +
104A TYR* 5.9 0.9 - - - -
148A ALA* 4.1 22.2 - - + -
163A ILE* 5.7 3.4 - - + -
188A ALA* 4.4 6.5 - - + -
189A HIS 3.2 11.9 - - - +
190A LEU* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 1.3 76.0 - - - +
39A ASN* 1.3 61.1 + - - +
40A VAL* 3.2 29.2 - - + +
102A SER* 3.4 12.1 + - - +
104A TYR* 5.1 12.0 + - + +
187A VAL 4.1 1.0 - - - +
188A ALA* 3.3 7.4 - - - -
189A HIS* 3.1 49.5 + - + -
408A CL 3.3 28.9 - - - +
----------------------------------------------------------
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