Contacts of the strand formed by residues 207 - 213 (chain B) in PDB entry 5MGS
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 ARG 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 3.1 26.9 + - - +
110B HIS* 3.9 20.3 + - - +
111B THR 3.3 17.5 - - - +
112B VAL* 4.2 14.7 - - + +
150B ILE* 3.7 43.3 - - + +
151B LEU 3.5 4.5 + - - +
152B PHE* 3.3 22.9 - - + -
153B TRP* 2.8 24.2 + - - -
206B ILE* 1.3 81.5 - - - +
208B TRP* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.7 1.4 - - - +
108B PHE* 3.8 0.2 - - - -
109B SER* 2.9 56.9 + - - -
111B THR* 3.2 34.8 - - - -
112B VAL 3.7 3.6 - - - -
113B ASN* 3.2 31.2 - - + -
118B SER* 3.5 35.4 - - - +
121B ASP* 2.9 49.0 + - + +
122B CYS* 3.7 8.3 - - - -
129B LEU* 4.1 2.9 - - + -
152B PHE* 4.0 1.8 - - - -
153B TRP* 3.6 17.0 - - + +
206B ILE 3.8 4.3 - - - -
207B ARG* 1.3 80.8 - - - +
209B ILE* 1.3 64.5 + - - +
210B CYS* 3.6 21.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.3 18.2 - - + -
107B LEU 3.3 7.2 - - - +
108B PHE* 3.6 37.7 - - + -
122B CYS* 4.3 0.2 - - - -
129B LEU* 3.5 9.7 - - - +
130B LEU* 3.0 48.6 + - + -
141B THR* 4.6 0.9 - - + -
145B ILE* 5.2 0.2 - - + -
152B PHE* 3.6 25.4 - - + -
153B TRP 3.2 9.0 + - - +
154B ILE* 4.8 0.2 - - + -
192B ILE* 3.8 24.2 - - + -
208B TRP* 1.3 79.5 - - - +
210B CYS* 1.3 73.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.8 11.8 - - + -
106B LEU* 3.3 5.2 - - - -
107B LEU* 2.9 38.2 + - + +
121B ASP* 3.8 5.8 - - - -
122B CYS* 2.1 50.7 - - - -
125B LYS* 4.8 6.1 - - - -
127B SER* 3.3 13.7 - - - +
128B SER 3.1 4.5 - - - -
208B TRP* 3.6 16.8 - - - -
209B ILE* 1.3 80.0 - - - +
211B GLN* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 4.3 3.5 + - - +
98B TRP* 4.0 0.9 - - - -
104B LYS* 3.0 27.5 + - + +
105B CYS 3.2 7.6 - - - +
106B LEU* 4.0 13.0 - - + -
127B SER* 3.2 7.3 - - - -
128B SER* 2.7 50.4 + - - +
129B LEU 4.0 3.1 - - - +
130B LEU* 3.4 6.7 - - + +
131B LEU* 2.9 43.1 + - - +
210B CYS* 1.3 74.1 - - - +
212B LYS* 1.3 63.6 + - - +
213B GLU* 3.5 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 3.5 12.8 + - - +
95B PRO* 4.8 17.0 - - + -
98B TRP* 3.6 33.4 - - + -
104B LYS* 3.5 2.4 - - - -
105B CYS* 2.8 42.4 + - + +
125B LYS 3.1 19.9 + - - -
126B GLU* 2.8 37.1 + - - +
127B SER* 4.0 0.7 - - - -
211B GLN* 1.3 79.4 - - - +
213B GLU* 1.3 63.0 - - - +
214B LEU* 3.7 0.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 2.8 25.4 + - - +
103B GLU 3.8 3.6 - - - +
104B LYS* 4.2 9.4 + - + +
131B LEU* 5.1 5.3 - - - +
133B ARG* 3.4 23.3 + - - +
211B GLN* 3.5 26.3 + - - +
212B LYS* 1.3 71.9 - - - +
214B LEU* 1.3 64.8 + - - +
215B THR 4.4 0.7 - - - +
216B PRO* 3.1 43.9 - - + +
217B VAL 4.6 1.5 + - - -
----------------------------------------------------------
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