Contacts of the strand formed by residues 138 - 143 (chain B) in PDB entry 3FVS
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 138 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY* 2.8 44.6 + - - +
116B ASP 2.7 13.8 + - - +
117B GLU* 3.3 17.3 + - + -
118B VAL 3.1 18.9 + - - -
132B THR* 4.0 2.4 - - - +
136B GLY 4.8 1.3 - - - +
137B GLY* 1.3 75.3 - - - -
139B PRO* 1.3 70.6 - - + +
140B VAL* 3.4 3.3 + - + +
174B ARG* 4.2 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL 3.6 7.2 - - - +
120B ILE* 4.0 11.7 - - + -
129B GLU* 4.1 15.0 - - + +
132B THR* 3.9 15.5 - - + -
133B MET* 4.0 22.4 - - + -
137B GLY 3.6 8.7 - - - +
138B ARG* 1.3 85.1 - - - +
140B VAL* 1.3 61.9 + - - +
141B PHE* 3.5 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 3.9 31.4 - - + +
118B VAL 2.8 11.3 + - - +
119B ILE* 3.2 10.8 - - + +
120B ILE* 2.8 25.3 + - - +
138B ARG* 3.8 10.8 - - + +
139B PRO* 1.3 79.6 - - - +
141B PHE* 1.3 63.6 + - - +
170B LYS* 3.9 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 5.4 0.2 - - - -
120B ILE* 3.4 22.4 - - + +
122B GLU* 4.0 21.5 - - + +
124B PHE* 3.5 35.2 - + - -
129B GLU* 3.7 18.6 - - - -
139B PRO* 3.5 37.2 - - + -
140B VAL* 1.3 74.4 - - - +
142B VAL* 1.3 59.3 + - - +
143B SER* 4.9 1.8 + - - -
170B LYS* 3.4 25.8 + - - -
386B SER* 3.5 26.9 - - - +
388B PRO* 6.1 0.2 - - + -
389B HIS* 5.0 8.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 4.0 12.8 - - + -
120B ILE 3.0 9.5 + - - +
121B ILE* 3.3 27.8 - - + +
122B GLU* 2.8 24.7 + - - +
140B VAL 4.0 0.8 + - - -
141B PHE* 1.3 74.5 - - - +
143B SER* 1.3 66.7 + - - +
144B LEU 4.0 0.5 + - - -
162B LEU* 4.1 21.1 - - + -
163B ASP 5.1 1.3 - - - +
166B GLU* 4.4 13.0 - - + +
167B LEU* 4.1 32.3 - - + +
170B LYS* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 2.6 32.2 + - - -
141B PHE 4.9 1.0 + - - -
142B VAL* 1.3 83.3 - - - +
144B LEU* 1.3 68.6 + - - +
145B LYS* 3.1 34.9 + - - +
161B GLN 4.2 1.4 - - - +
162B LEU* 5.6 0.6 - - - -
163B ASP 5.5 1.4 + - - -
166B GLU* 3.9 2.2 + - - +
385B TYR* 5.3 0.7 - - - -
389B HIS* 3.6 15.6 + - - -
393B PHE* 4.8 13.9 - - - -
----------------------------------------------------------
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