Contacts of the strand formed by residues 145 - 151 (chain I) in PDB entry 5DSV
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 145 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ARG* 6.0 0.7 - - - -
139I SER* 3.9 1.6 + - - +
140I TYR* 3.5 12.8 - - - -
141I SER 2.9 34.5 + - - +
142I VAL 3.6 6.8 + - - -
143I ASN 3.5 1.4 - - - -
144I ASP* 1.3 84.5 - - - +
146I ALA* 1.3 59.9 - - - -
147I GLN* 4.0 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ARG* 3.1 41.0 + - + +
41I CYS 4.3 2.9 - - - +
42I LYS 4.7 5.3 + - - +
44I GLY* 3.5 41.3 - - - +
45I VAL* 4.2 0.2 - - + -
139I SER 3.6 5.6 - - - -
140I TYR* 3.5 8.7 - - + -
144I ASP 4.5 1.6 - - - +
145I GLY* 1.3 69.7 - - - -
147I GLN* 1.3 69.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ARG* 4.4 5.6 - - - +
45I VAL* 3.4 6.9 - - - +
107I PRO* 5.5 0.2 - - - +
108I LEU* 3.4 37.8 - - + +
109I LYS* 3.6 35.5 - - - +
138I GLY* 3.3 5.0 - - - -
139I SER* 3.0 37.3 + - - +
144I ASP* 3.8 36.0 + - - +
145I GLY 4.0 8.3 - - - +
146I ALA* 1.3 82.5 - - - +
148I LEU* 1.3 61.0 + - - +
149I TYR* 4.0 9.7 + - + -
59J GLU* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLY 3.7 9.6 - - - +
39I ILE* 3.9 6.3 - - - +
40I ARG* 4.6 6.1 - - + +
45I VAL* 3.9 14.4 - - + -
47I PHE* 3.5 38.6 - - + -
136I MET* 4.3 13.7 - - + -
137I LEU 3.4 7.2 - - - +
147I GLN* 1.3 77.4 - - - +
149I TYR* 1.3 66.0 + - - +
159I GLY* 3.5 4.5 - - - -
160I TYR* 2.9 54.4 + - + +
161I TRP 4.0 2.7 - - - +
162I GLY* 3.7 30.1 - - - -
163I CYS 4.0 2.7 - - - +
59J GLU* 5.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I LEU* 3.7 20.4 - - + -
109I LYS* 3.4 47.0 - - - +
112I ALA* 3.9 19.5 - - + -
136I MET* 2.9 9.8 - - - +
137I LEU* 2.8 44.6 + - + +
147I GLN* 4.0 15.7 + - + -
148I LEU* 1.3 81.2 - - - +
150I MET* 1.3 58.9 + - - +
151I ILE* 4.4 2.2 - - + -
157I SER* 3.6 17.5 - - - +
158I TYR* 3.2 19.1 - - - -
159I GLY* 3.4 21.3 - - - -
160I TYR* 5.0 0.7 - - - +
59J GLU* 5.1 6.1 + - - -
61J GLY 5.7 1.0 + - - -
62J SER* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I SER* 4.4 1.6 - - - -
135I PHE 3.3 10.8 - - - +
136I MET* 4.0 20.9 - - + -
149I TYR* 1.3 75.1 - - - +
151I ILE* 1.3 78.2 + - - +
152I ASP* 3.9 19.5 - - + +
156I VAL 3.3 3.7 - - - +
157I SER* 3.7 0.3 - - - -
158I TYR* 2.8 56.3 + - + -
160I TYR* 3.9 27.1 - - + +
163I CYS* 4.6 6.7 - - - -
165I ILE* 4.1 23.8 - - + -
169I ARG* 5.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ALA* 4.0 34.5 - - + +
115I VAL* 5.2 0.4 - - + -
116I ALA* 4.0 9.2 - - + +
119I VAL* 4.1 16.6 - - + -
134I SER* 3.2 5.5 - - - -
135I PHE* 2.9 75.4 + - + +
137I LEU* 4.4 5.6 - - + -
149I TYR* 5.1 0.4 - - + -
150I MET* 1.3 84.5 - - - +
152I ASP* 1.3 74.7 + - - +
155I GLY* 4.4 6.3 - - - -
156I VAL 3.3 12.6 - - - +
157I SER* 3.8 12.8 - - - +
----------------------------------------------------------
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