Contacts of the strand formed by residues 49 - 58 (chain L) in PDB entry 5D4D
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 PRO 49 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L SER 3.3 9.4 - - - +
48L ILE* 1.3 88.5 - - + +
50L GLY* 1.3 57.8 - - - +
146L ARG* 5.3 11.4 - - + -
147L GLY 3.7 0.9 - - - +
148L VAL* 3.7 14.8 - - + -
173L PRO* 3.8 11.0 - - - +
205L VAL* 4.3 8.3 - - - +
213L GLN* 3.2 26.8 + - - +
217L ILE* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L ILE 3.6 1.2 + - - -
49L PRO* 1.3 75.2 - - - +
51L THR* 1.3 65.6 + - - -
146L ARG* 3.3 11.3 - - - +
147L GLY 2.9 33.0 + - - -
171L PHE 3.3 16.6 - - - -
173L PRO* 4.1 7.4 - - - -
204L SER* 6.0 0.7 - - - -
205L VAL* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L GLY* 1.3 80.2 - - - +
52L ALA* 1.3 64.2 + - - +
85L LEU 5.6 1.7 - - - +
87L VAL* 2.5 43.3 + - - +
88L ARG* 4.9 0.4 - - - -
89L PHE* 4.1 33.0 - - + +
144L VAL* 4.3 11.2 - - - +
145L ASP 3.4 9.6 - - - -
146L ARG* 4.7 6.3 - - - +
170L VAL 3.4 9.8 - - - +
171L PHE* 3.5 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L THR* 1.3 75.7 - - - +
53L VAL* 1.3 63.0 + - - +
54L THR* 3.4 2.4 + - - +
85L LEU 6.0 2.0 - - - -
144L VAL* 3.3 5.6 - - - +
145L ASP 2.8 33.6 + - - +
169L ALA* 4.0 5.4 - - + -
170L VAL 3.2 39.9 - - - +
171L PHE* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L ALA* 1.3 72.3 - - - +
54L THR* 1.3 59.5 + - - +
55L SER 3.9 19.5 - - - +
56L VAL* 4.0 16.6 - - + -
82L LEU* 3.8 30.5 + - + +
83L LYS* 5.5 2.0 - - - +
85L LEU* 4.2 18.6 + - + +
87L VAL* 5.8 0.9 - - + -
142L VAL* 4.4 9.4 - - + -
143L ARG 3.2 4.9 - - - +
144L VAL* 3.7 21.5 - - + -
167L VAL* 3.6 26.3 - - + +
168L ASP 4.0 6.1 - - - +
169L ALA* 4.2 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L ALA 3.4 2.4 + - - +
53L VAL* 1.3 74.3 - - - +
55L SER* 1.3 57.7 + - - -
143L ARG* 2.7 23.5 + - - +
145L ASP* 3.1 32.8 + - + +
156L HIS* 2.9 37.0 - - + +
158L ILE* 3.3 13.7 - - + +
167L VAL 3.0 14.0 + - - -
169L ALA* 3.7 24.9 - - + -
171L PHE* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L VAL* 3.6 3.2 - - - +
54L THR* 1.3 81.3 + - - +
56L VAL* 1.3 71.2 + - - +
142L VAL* 3.4 0.9 - - - +
143L ARG* 2.8 39.5 + - - -
158L ILE* 3.8 23.1 + - - -
159L LYS* 4.8 1.1 - - - -
160L ASP* 5.0 3.5 + - - -
164L ALA* 3.4 22.7 - - - +
165L ILE 3.3 16.1 + - - -
166L PRO* 4.2 0.2 - - - -
167L VAL* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L VAL* 4.0 4.5 - - + -
55L SER* 1.3 82.6 + - - +
57L TYR* 1.3 60.9 + - - +
58L ILE* 3.7 30.0 + - + -
79L ILE* 5.3 6.5 - - + -
82L LEU* 3.5 28.0 - - + -
140L MET* 4.2 2.9 - - - -
141L GLU 3.4 10.5 - - - +
142L VAL* 3.6 14.6 - - + -
164L ALA* 4.0 2.7 - - - -
165L ILE* 2.4 52.8 + - + +
167L VAL* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L VAL* 1.3 73.1 - - - +
58L ILE* 1.3 72.7 + - - +
59L GLU* 4.1 29.6 - - + +
60L ASP 4.4 4.1 + - - -
140L MET* 3.2 6.0 - - - +
141L GLU* 2.9 49.5 + - + +
161L ARG* 3.5 51.1 + - + +
162L ILE* 5.7 0.7 - - + -
163L ASN* 3.4 46.0 + - + -
164L ALA* 3.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L VAL* 3.7 20.6 + - + +
57L TYR* 1.3 91.2 - - - +
59L GLU* 1.3 69.9 + - - +
60L ASP 3.3 0.7 + - - -
61L VAL* 3.0 45.3 + - + +
68L ILE* 3.9 22.2 - - + -
75L VAL* 4.5 20.9 - - + -
78L ILE* 4.7 7.9 - - + -
79L ILE* 5.7 2.2 - - + -
138L LEU* 4.2 9.9 - - + -
139L ASN 3.8 9.0 - - - +
140L MET* 3.6 25.4 - - + -
163L ASN 5.2 1.0 + - - -
165L ILE* 5.5 5.0 - - + +
----------------------------------------------------------
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